• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2004.10a
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• pp.539-542
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• 2004

배낭 문제는 조합 최적화 문제로서, 다항 시간(polynomial time)에 풀리지 않는 NP-hard 문제이다 이 문제를 해결하기 위해 기존에는 DNA 컴퓨팅 기법과 GA 등을 사용하여 해결하였다. 하지만 기존의 방법들은 DNA의 정확한 특성을 고려하지 않아, 실제 실험과의 결과 차이가 발생하고 있다. 본 논문에서는 DNA 컴퓨팅 실험 과정에서 발생하는 DNA 조작 오류를 최소화하고, 보다 정확한 예측을 위해 함수 언어인 Haskell을 이용한 코드 최적화 DNA-Haskell을 제안한다. 코드 최적화 DNA-Haskell은 배낭 문제 중 (0,1)-배낭 문제에 적용하였고, 그 결과 기존의 DNA 컴퓨팅 방법보다 실험적 오류를 최소화하였으며, 또한 적합한 해를 빠른 시간 내에 찾을 수 있었다.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1225-1228
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• 2006

Cyclic AMP receptor protein (CRP) complexed with cAMP binds to DNA and induces sharp DNA bending around ${\sim}90$ degree. Previous publication (5), however, reported that mutant CRP:cGMP complex showed high migration rate relative to mutant CRP:cAMP complex on native polyacrylamide gel. To confirm DNA structural change in the presence of CRP and cyclic nucleotide, molar cyclization factor $(j_M)$ [13] was measured with 6 constructed DNA fragments. Nonlinear regression analysis of $j_M$ data indicated that mutant CRP did not induce DNA bending in the presence of cGMP but bent DNA in the presence of cAMP without any helical twist change in DNA.

• Journal of Life Science
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• v.31 no.12
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• pp.1057-1065
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• 2021

Alterations in mitochondrial DNA (mtDNA) copy numbers have been reported in patients with stomach cancer and suggested to play a role in gastric carcinogenesis or gastric cancer progression. However, changes in the levels of mitochondrial proteins or mtDNA-encoded oxidative phosphorylation (OXPHOS) proteins in gastric cancer remain unclear. In this study, we investigated mtDNA contents, mitochondrial protein levels, and mtDNA-encoded OXPHOS protein levels in gastric cancer tissues and cell lines. We correlated mtDNA copy numbers with clinicopathologic features of the gastric cancer samples used in this study and used quantitative PCR to analyze the mtDNA copy numbers of the gastric cancer tissues and cell lines. Western blot analysis was used for assessing the amounts of mitochondrial proteins and mtDNA-encoded OXPHOS proteins. Among the 27 gastric cancer samples, 22 showed a reduction in mtDNA copy numbers. The mtDNA content was increased in the other five samples relative to that in normal matched gastric tissues. Mitochondrial protein and OXPHOS protein levels were reduced in some gastric cancer tissues. However, mitochondrial protein and OXPHOS protein levels in gastric cancer cell lines were not always in line with their mtDNA contents. The mtDNA copy numbers were reduced in five gastric cancer cell lines tested in this study. In summary, this study reports a common reduction in mtDNA contents in gastric carcinoma tissues and cell lines, pointing to the possible involvement of mtDNA content alterations in tumorigenesis of the stomach.

• The Korean Journal of Zoology
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• v.26 no.1
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• pp.19-28
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• 1983

Alkaline elution profiles showed that the frequency of DNA single strand breaks associated with DNA-protein crosslinks in cells treated with both an inducing dose of MMC $(MMC_1)$ and a challenge dose of MMC $(MMC_2)$ was slightly less than that in cells treated with MMC alone. The amount of unscheduled DNA synthesisi in cells treated with both $MMC_1$ and $MMC_2$ was greater than that in cells treated with MMC alone. This enhancement of exicision repair detected by UDS autoradiography and alkaline elution, was not observed, when cells were incubated with cyclohexmide between the two treatments of $MMC_1$ and $MMC_2$. These results suggest that MMC-damaged DNA from Chinses hamster cells is repaired by excision repair mechanisms that require de novo protein synthesis for enhancement, and that an inducible repair mechanism may exist in CHO cells.

• 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.

• Biomedical Science Letters
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• v.11 no.2
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• pp.103-108
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• 2005

2-Deoxyribonolactone (dL) arises as a major DNA damage induced by a variety of agents, involving free radical attack and oxidation of C1'-deoxyribose in DNA. We investigated whether dL lesions can be repaired in mammalian cells and the mechanisms underlying the role of DNA polymerase $\beta$ in processing of dL lesions. Pol $\beta$ appeared to be trapped by dL residues, resulting in stable DNA-protein cross-links. However, repair DNA synthesis at site-specific dL sites occurred effectively in cell-free extracts, but predominantly accompanied by long-patch base excision repair (BER) pathway. Reconstitution of long-patch BER demonstrated that FEN1 was capable of removing the displaced flap DNA containing a 5'-dL residue. Cellular repair of dL lesions was largely dependent on the DNA polymerase activity of Pol $\beta$. Our observations reveal repair mechanisms of dL and define how mammalian cells prevent cytotoxic effects of oxidative DNA lesions that may threaten the genetic integrity of 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.

• Microbiology and Biotechnology Letters
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• v.41 no.4
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• pp.456-461
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• 2013

Using the different adsorption properties of ssDNA and dsDNA to GO, this study used a real time and efficient fluorescence assay to detect the enzymatic activity of the Klenow fragment with the adsorbed DNA to GO. Results showed that adsorption of fluorescein-tagged ssDNA to GO resulted in fluorescence quenching and DNA was released from GO by adding complementary DNA. In addition, fluorescence restoration was increased through a polymerization reaction by the Klenow fragment in the presence of a fluorescein-attached template, GO, and primer. Gel electrophoresis was conducted to confirm the hybridization and DNA polymerization reactions on GO.

• Journal of the Institute of Electronics Engineers of Korea SC
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• v.48 no.3
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• pp.53-59
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• 2011

Charge transfer through DNA oligonucleotides has been investigated for potential applications of DNA into molecular electrooptic switching devices. Electrons were injected using gold electrode probes where DNA oligomers were adsorbed that are separated in medium. The results show that increased adsorption of DNA reduces the ionization current due to the combined effect of charge transfer through DNA and surface-limited charge transport. The probe-based charge injection was extended to examine the capability of extinguishing fluorescence of Cy3 dye molecules attached to DNA. It is expected that the results may be employed to implementing a novel electrooptic switching device based on DNA molecules.

• Journal of KIISE:Computer Systems and Theory
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• v.36 no.4
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• pp.231-238
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• 2009

DNA sequences are the fundamental information for each species and a comparison between DNA sequences of different species is an important task. Since DNA sequences are very long and there exist many species, not only fast matching but also efficient storage is an important factor for DNA sequences. Thus, a fast string matching method suitable for encoded DNA sequences is needed. In this paper, we present a fast string matching method for encoded DNA sequences which does not decode DNA sequences while matching. We use four-characters-to-one-byte encoding and combine a suffix approach and a multi-pattern matching approach. Experimental results show that our method is about 5 times faster than AGREP and the fastest among known algorithms.