• ETRI Journal
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• v.30 no.6
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• pp.818-825
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• 2008

This paper proposes an exponentiation method with Frobenius mappings. The main target is an exponentiation in an extension field. This idea can be applied for scalar multiplication of a rational point of an elliptic curve defined over an extension field. The proposed method is closely related to so-called interleaving exponentiation. Unlike interleaving exponentiation methods, it can carry out several exponentiations of the same base at once. This happens in some pairing-based applications. The efficiency of using Frobenius mappings for exponentiation in an extension field was well demonstrated by Avanzi and Mihailescu. Their exponentiation method efficiently decreases the number of multiplications by inversely using many Frobenius mappings. Compared to their method, although the number of multiplications needed for the proposed method increases about 20%, the number of Frobenius mappings becomes small. The proposed method is efficient for cases in which Frobenius mapping cannot be carried out quickly.

• Proceedings of the KSRS Conference
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• 2005.10a
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• pp.280-282
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved algorithm provides better levels of performance than the originals.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.143-148
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• 2015

In some pathogenic bacteria, there are RNA thermometers, which regulate the production of virulence associated factors or heat shock proteins depending on temperature changes. Like a riboswitches, RNA thermometers are located in the 5'-untranslated region and involved translational gene regulatory mechanism. RNA thermometers block the ribosome-binding site and start codon area under the $37^{\circ}C$ within their secondary structure. After bacterial infection, increased the temperature in the host causes conformations changes of RNA, and the ribosome-binding site is exposed for translational initiation. Because structural differences between open and closed forms of RNA thermometers are mainly mediated by base pairing changes, NMR spectroscopy is a very useful method to study these thermodynamically changing RNA structure. In this review, we briefly provide a fundamental function of RNA thermometers, and also suggest a proper NMR experiments for studying RNA thermometers.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.213.1-213.1
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• 2015

Field effect transistors (FETs)를 기반으로 한 바이오센서는 빠른 응답속도, 저비용, label-free 등을 이유로 각광받고 있다. 그러나 3D 구조를 기반으로 한 FETs 바이오센서의 낮은 sensitivity의 한계점을 지니며, 이를 극복하기 위해 1D 구조의 나노튜브 등을 활용하였으나 여전히 높은 sensitivity의 확보는 힘들다. 최근에는 이러한 문제점을 극복하기 위해 이차원 반도체 물질 중 하나인 Transition metal dichalcogenide (TMD)를 이용하여, 700 이상의 sensitivity를 지니는 pH센서 및 100 이상의 sensitivity를 지니는 바이오센서가 보고되었다. 하지만 이보다 더 높은 정확성 및 반응성을 높이기 위한 연구는 부족한 실정이다. 우리는 DNA 템플릿을 이용하여, TMD FET 기반 pH 및 바이오센서의 반응성을 극대화시키는 연구를 선보인다. DNA는 7~8정도의 유전상수 (K)를 가지는 물질로 기존 $SiO_2$(K=3.9)보다 높은 유전상수를 가지며 두께를 0.7 nm로 매우 얇게 형성할 수 있는 장점이 있다. 이는 FET 기반 바이오센서의 표면 캐패시턴스를 높여 sensitivity를 극대화할 수 있으며, 기존에 사용된 high-k 기반 바이오센서와 비교하여도 약 10배 이상의 sensitivity 향상을 노릴 수 있다. 또한, TMD 물질로 우리는 $WSe_2$를 선택하였으며, pH 용액의 receptor로써 우리는 3-Aminopropyltriethoxysilane (APTES)를 활용하였고, 템플릿으로 사용된 DNA는 DX tile 및 Ring type의 두 가지를 사용하였다. 추가로, DNA의 phosphate backbone을 중성화시키고 DNA의 base pairing의 charge 안정화를 위해 구리 이온($Cu^{2+}$) 및 란타넘족($Tb^{3+}$)을 추가하였다. 완성된 바이오센서의 pH 센싱을 위해 우리는 pH 6,7,8의 표준 용액을 사용하였으며, 재현성 및 반복성의 확인하였다.

• Bulletin of the Korean Chemical Society
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• v.29 no.10
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• pp.1937-1940
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• 2008

The P1 duplex of Tetrahymena group I ribozyme is the important system for studying the conformational changes in folding of ribozyme. The formation of the P1 duplex between IGS and substrate RNA and the catalytic activity of ribozyme require a variety of metal ions such as $Mg^{2+}$ and $Mn^{2+}$. In order to investigate the effect of the $Mg^{2+}$ concentration on the conformation of the P1 duplex, the NMR study was performed as a function of $Mg^{2+}$ concentration. This study revealed that the less stable AU-rich region formed duplex at $50{^{\circ}C}$ under high $Mg^{2+}$ concentration condition but melts out under low $Mg^{2+}$ concentration condition. It was also found that in the active conformation under 10 mM $MgCl_2$ condition, the unstable central G${\cdot}$U wobble pair maintains the significant base pairing up to $50{^{\circ}C}$. This study provides the information of the unique feature of the P1 duplex structure and the roll of $Mg^{2+}$ ion on the formation of the active conformation.

• BMB Reports
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• v.31 no.2
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• pp.177-182
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• 1998

A pool of cis-acting hammerhead ribozymes randomized in their substrate recognition sequences was constructed. A variety of active cis-acting ribozymes which had various structures of stems I and III was selected from the pool by in vitro selection. The selected ribozymes were cloned and sequenced. The relationship between the cleavage efficiency and base-pairing in stems I and III of the selected ribozymes was investigated. The ribozymes with the smaller difference in folding energies between the active conformation and the stable but inactive conformation showed a tendency to have the better cleavage efficiency. The optimum length of stem I was 5 or 6 bases while the longer stem III, in general, appeared to be required for efficient cleavage. The specificity of the ribozyme reaction is discussed in terms of the length of stems I and III.

• Proceedings of the Korea Information Processing Society Conference
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• 2005.11a
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.889-892
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• 2000

Antisense molecules are structurally simple linear oligomers of nucleotides. They can recognize a complementary sequence by base pairing, therefore, antisense drugs composed of 15-16 bases are potentially useful, unlike drugs such as protein agonists, antagonists, and inhibitors. Since antisense oligomers are classified as nucleotides, they are subject to attack by nucleases. In order to be antisense drugs resistant to degradation by nucleases, the structural modifications in the linkages, bases, and sugars to satisfy this requirement are considerable. We attempted in this study, to synthesize 16-mer antisenses with a modified linkage and adenosine. When studying on the three-dimensional structure of the oligomer, however, the existence of isomers may complicate the interpretation of the NMR data. Therefore, an attempt was made to eliminate the above problem, thus, two dimers were synthesized and their structural studies were carried out.

• Journal of Microbiology and Biotechnology
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• v.16 no.4
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• pp.569-575
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• 2006

The 530 stem-loop is a 46 nucleotide stem-loop structure found in all small-subunit ribosomal RNAs. Phylogenetic and mutational studies by others suggest the requirement for Watson-Crick interactions between the nucleotides 505-507 and 524-526 (530 pseudoknot), which are highly conserved. To examine the nature and functional significance of these interactions, a random mutagenesis experiment was conducted in which the nucleotides in the proposed pseudoknot were simultaneously mutated and functional mutants were selected and analyzed. Genetic analysis revealed that the particular nucleotide present at each position except 524 was not exclusively critical to the selection of functional mutants. It also indicated that basepairing interactions between the positions 505-507 and 524-526 were required for ribosomal function, and much weaker base-pairing interactions than those of the wild-type also allowed high ribosomal function. Our results support the hypothesis that the 530 pseudoknot structure may undergo a 'conformational switch' between folded and unfolded states during certain stages of the protein synthesis process by interacting with other ligands present in its environment.

• Herbal Formula Science
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• v.16 no.1
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• pp.65-78
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• 2008

Objectives : this study was to access the effect of Hyeonggaeyeongyotang water extracts, a polyherbal formula has been used as folk medicine, on the fertility and early embryonic development of male and female Wistar rats when administered by oral gavage. Methods : In male rats, Hyeonggaeyeongyotang extract were dosed 4 weeks before pairing and 2 weeks after mating including the mating periods up to termination after necropsy of the majority of the females. In female rats, they were dosed 2 weeks before pairing, and from Day 0 to Day 7 of gestation. This study was conducted in accordance with the recommendations of the KFDA Guideline [2005-60] for Detection of Toxicity to Reproduction for Medicinal Products. Results: 1. No Hyeonggaeyeongyotang extract treatment-related changes on the clinical signs and mortalities, the Food consumptions, the Body weights and gains were demonstrated in all dosed levels tested in this study except for 500ml/kg-dosing male group in which a significant(p<0.05) increase of body gains was detected during day 0-7 after dosing. 2. No Hyeonggaeyeongyotang extract treatment-related changes on the pre-coital intervals, the estrus cycles, the mating index, conception rate and fertility index were demonstrated in all dosed levels tested in this study. 3. No Hyeonggaeyeongyotang extract treatment-related gross findings on reproductive organs, the weights of reproductive organs, histopathological findings on reproductive organs, the corpora lutea number, implantation site number, live fetus number, number of resorpted embryo and pre-and post-implatation loss were demonstrated in all dosed levels tested in this study. Conclusions : Base on the results, it is considered that the NOAEL (No-Observed-Adverse-Effect Level) for fertility and early embryonic development toxicity of Hyeonggaeyeongyotang extract was under 2000ml/kg/day in Wistar male and female rats because there no treatment-related changes on the fertility and early embryonic developmental index were demonstrated in all dosed levels tested.