• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.17 no.2
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• pp.87-102
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• 2013

An n-string tangle is a three dimensional ball with n-strings which are properly embedded in the ball. In early 90's, C. Ernst and D. Sumners first used a tangle to describe a DNA-protein complex. In this model, DNA is represented by a string and protein is represented by a ball. Mu is a protein which binds to DNA at three sites and a DNA-Mu complex is called Mu-transpososome. Knowing the DNA topology within Mu-transpososome is very important to understand DNA transposition by Mu protein. In 2002, Pathania et al. determined that the DNA configuration within the Mu transpososome is three branched and five noded [12]. In 2007, Darcy et al. analyzed this by using mathematical tangle and concluded that the three branched and five noded DNA configuration is the only biologically reasonable solution [4]. In this paper, based on the result of Pathania et al. and Darcy et al., the author determines the DNA topology within the DNA-Mu complex after the whole Mu transposition process. Furthermore, a new experiment is designed which can support the Pathania et al.'s result. The result of this new experiment is predicted through mathematical knot thory.

• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.15 no.3
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• pp.161-175
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• 2011

An n-string tangle is a three dimensional ball with n strings properly embedded in it. A tangle model of a DNA-protein complex is first introduced by C. Ernst and D. Sumners in 1980's. They assumed the protein bound DNA as strings and the protein as a three dimensional ball. By using a tangle analysis, one can predict the topology of DNA within the complex. S.Kim and I. Darcy developed the biologically reasonable 4-string tangle equations and decided a solution tangle, called R-standard tangle. The author discussed more about the simple solution tangles of the equations and found a generalized R-standard tangle solution.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.314.2-314.2
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• 2002

DNA topoisomerases catalyze changes in DNA topology through cycles of transient DNA strand breakage and religation. During this process. the active site tyrosine in human DNA topoisomerase Ⅰ(Top Ⅰ) becomes covalently linked to the 3'-ends of a single-stranded nick in the DNA duplex, Stabilization of the Top Ⅰ-DNA cleavable complex is the common initial event leading to the cytotoxicity of top 1 inhibitors. (omitted)

• Journal of applied mathematics & informatics
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• v.35 no.3_4
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• pp.349-369
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• 2017

In last 30 years, mathematical tangle theory is applied to molecular biology, especially to DNA topology. The recent issues and research results of this topic are reviewed in this paper. We introduce a tangle which models an enzyme-DNA complex. The studies of 2-string tangle equations related to Topoisomerase II action and site-specific recombination is discussed. And 3-string tangle analysis of Mu-DNA complex, n-string tangle analysis ($n{\geq}4$) of DNA-enzyme synaptic complexes are also discussed.

• BMB Reports
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• v.39 no.5
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• pp.522-529
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• 2006

Silk moths are the best studied silk secreting insects and belong to the families Bombycidae and Saturniidae. The phylogenetic relationship between eleven silk producing insects was analyzed using the complete DNA sequence of the internal transcribed spacer DNA 1 locus. The PCR amplification and sequence analysis showed variation in length ranging from 138 bp (Antheraea polyphemus) to 911 bp (Hyalopora cecropia). Microsatellite sequences were found and was be used to distinguish Saturniidae and Bombycidae members. The nucleotide sequences were aligned manually and used for construction of phylogenetic trees based on Maximum parsimony and Maximum likelihood methods. The topology in both the approaches yielded a similar tree that supports the ancestral position of the Antheraea assama.

• BMB Reports
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• v.32 no.4
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• pp.409-413
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• 1999

The cDNA encoding CMP-NeuAc:lactosylceramide ${\alpha}2$,3-sialyltransferase (GM3 synthase) was isolated from a human fetal brain cDNA library using sequence information obtained from amino acid sequences found in the conserved regions of the previously-cloned mouse GM3 synthase (mST3Gal V) and human sialyltransferases. The cDNA sequence included an open reading frame coding for 362 amino acids, and the primary structure of this enzyme predicted all the structural features characteristic of other sialyltransferases, including a type II membrane protein topology and both sialylmotifs. Comparative analysis of this cDNA with mST3Gal V showed 85% and 86% identity of the nucleotide and amino acid residues, respectively. The expression of this gene is highly restricted in both human fetal and adult tissues.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.6
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• pp.565-571
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• 2000

Mixed primers based on the high sequence homology of selected regions of known connexins (Cxs) was used for PCR reaction. A full-length connexin cDNA of sweetfish (Plecoglossus altivelis) was cloned by rapid amplification of cDNA 5'and (5'RACE) and 3'RACE method. When compared to other known Cx sequences, homology of sweetfish Cx cDNA to Atlantic croaker, Mycropogonias undulatus Cx32.7, bovine, Bos taurus Cx44 and Atlantic croaker Cx32.2 were $63.8{\%},\;61.6{\%}\;and\;56.7{\%}$, respectively. This cDNA encoded 308 amino acids (35,028 dalton) and named as sweetfish Cx35. Hydropathicity analysis of predicted amino acid sequences indicated that sweetfish Cx35 have four major hydrophobic regions and four major hydrophilic regions, suggesting its topology is similar to that of known Cxs. The presence of a tfical Cx consensus sequences were identified in each of the extracellular loops (first loop and second loop).

• Korean Institute of Interior Design Journal
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• v.14 no.3 s.50
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• pp.64-72
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• 2005

The purpose of this study is to propose a topological design principles and to analyze the space of digital architecture applying topological invariant expressive characteristics. As this study is based on topology as a science of true world's pattern, we intented to explain the concepts and provide some methods of low-level and hyperspace topological invariant Properties. Four major aspects are discussed. Those are connection theory, boundary concept, homotopy group, knot Pattern theory as topological invariant properties. Then we intented to make understand topological characteristics of the Algorithms, luring machine, cellular automata, string theory, membrane, DNA and supramolecular chemistry. In fine, the topological invariant properties of the digital architecture as genetic algorithms based on self-organization and heterogeneous networks of interacting actors can be analyzed and used as a critical tool. Therefore topology can be provided endless possibilities for architecture, designers and scientists intended in expressing the more complex and organic patterns of nature as life.

• Journal of the Korean Mathematical Society
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• v.51 no.4
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• pp.817-836
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• 2014

We develop a topological model of site-specific recombination that applies to substrates which are the connected sum of two torus links of the form T(2, n)#T(2, m). Then we use our model to prove that all knots and links that can be produced by site-specific recombination on such substrates are contained in one of two families, which we illustrate.

• Journal of Life Science
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• v.11 no.2
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• pp.74-80
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• 2001

The nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA (rDNA), and the 5.85 rRNA gene, have been determined for 13 strains of dinoflagellates in order to analyze the phylo-genetic relationship. The DNA sequences contained considerable variation in the ITS regions, but little in the 5.85 rDNA. In addition, the ITS1 was more variable than the ITS2 in all species examined. The nucleotide length of this region varied from 519 bp to 596 bp depending on the taxa. The investigated taxa were divided into three large groups based on the ITS length, i. e., a group with short ITS region (A. fraterculus and Alexandrium sp.), a with ITS region group (P. micans, P. minimum and P. triestinum) and a with ITS region group (G. impudicum, C. polykrikoides, G. sanguineum, G. catenatum and H. triquetra). The relationship between nucleotide length of ITS1 and that of ITS2 was negative, whereas G+C content and nucleotide length showed positive correlation. In phylogenetic analyses producing NJ trees, the topology was similar cluster and clearly divided the taxa into three groups based on 5.8S rDNA that were similar to those based on morphological characteristics. In particular, G. impudicum was more closely related to G. catenatum than to C. polykrikoides using phylogenetic analysis. From this study, we chew that the length of ITS region contributes to discriminate Korean harmful algal species and ITS analysis is a useful method for resolving the systematic relationships of dinoflagellates.