• 대한전기학회논문지:전기물성ㆍ응용부문C
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• 제51권6호
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• pp.265-270
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• 2002

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and application area. So, the improvement of DNA hybridization detection method is very important for the determination of this hybridization reaction. Several molecular biological techniques require accurate predictions of matched versus mismatched hybridization thermodynamics, such as PCR, sequencing by hybridization, gene diagnostics and antisense oligonucleotide probes. In addition, recent developments of oligonucleotide chip arrays as means for biochemical assays and DNA sequencing requires accurate knowledge of hybridization thermodynamics and population ratios at matched and mismatched target sites. In this study, we report the characteristics of the probe and matched, mismatched target oligonucleotide hybridization reaction using thermodynamic method. Thermodynamic of 5 oligonucleotides with central and terminal mismatch sequences were obtained by measured UV-absorbance as a function of temperature. The data show that the nearest-neighbor base-pair model is adequate for predicting thermodynamics of oligonucleotides with average deviations for $\Delta$H$^{0}$ , $\Delta$S$^{0}$ , $\Delta$G$_{37}$ $^{0}$ and T$_{m}$, respectively.>$^{0}$ and T$_{m}$, respectively.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2003년도 가을 학술발표논문집 Vol.30 No.2 (2)
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• pp.772-774
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• 2003

DNA/DNA의 연쇄 결합 반응에 대한 시뮬레이션을 열역학적 데이터를 이용하여 구현하였다. 1-Base의 non Watson-Crick 결합과, dangling end(결합이 이루어진 두개의 DNA strand 중 한쪽 끝이 다른 쪽 끝보다 길거나 짧은 경우)를 허용하는 nearest-neighbor model을 사용하여 구현된 이 모델에서는 한번의 hybridization만을 예측하는 것이 아니라 연속적인 결합 반응의 시뮬레이션이 가능하다. 이를 통해서 분자 알고리즘의 설계와 검증이 가능할 뿐만 아니라, cross-homology의 검사를 통한 시퀀스의 검증까지도 가능하다. 이러한 in silico 에서의 접근 방식은 효율적인 분자 알고리즘의 개발과 신뢰성 있는 시퀀스의 설계에 도움이 될 수 있다.

• BMB Reports
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• 제34권1호
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• pp.59-65
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• 2001

In subtractive hybridization, target sequences in the tester are enriched by hybridizing with an excess amount of driver, followed by removing the tester hybridized with the driver. All of existing subtractive cloning methods are designed to remove the tester/driver hybrid. The removal of hybrid, however, is often unsatisfactory For various reasons. In this study we developed a subtractive enrichment protocol in which the tester/driver can be completely removed by selecting only the tester/tester after hybridization. In this protocol both the tester and driver DNAs are ligated with same linker DNAs and amplified by polymerase chain reaction (PCR). The tester DNA is then digested with two different enzymes and used in subsequent hybridization with an excess driver. After hybridization, the DNA is ligated with the adaptor that is only compatible with the tester/tester. Since only the tester/tester can have the new adaptor, no tester/driver can be amplified by PCR in this protocol. Unlike other methods, a 100% subtraction efficiency can be achieved even though the enzymatic treatments used in the enrichment procedure are incomplete. Furthermore, only the hybridized tester DNA can have the new adaptor and be amplified by PCR, resulting in 100% denaturation in effect. The efficacy of this novel method was verified with the model system in which a known amount of the target sequence is included.

• 식물조직배양학회지
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• 제25권5호
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• pp.323-327
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• 1998

페튜니아에서의 안토시아닌 생합성 경로는 하나의 중요한 유전적인 모델시스템으로 연구되어 왔다. 본 연구에서는 이 경로에 대한 유전자를 연구하기 위하여 CaMV 35S promoter와 가지로부터 분리된 flavonoid 3',5'-hydroxylase cDNA를 pBI121 플라스미드에서 fusion gene 시스템을 만들었다. 형질전환된 페튜니아를 얻기 위한 최적조건이 페튜니아 절간을 IAA 0.2 ㎎/mL, BA 3 ㎎/mL를 혼용한 MS배지에서 얻었다. 효과적인 형질전환을 위하여 페튜니아 절간을 IAA 0.2㎎/L BA 3㎎/L를 혼용한 BM배지에서 Agrobacterium tumefaciens를 접종하기 전에 절편체를 preculture하였다 형질전환체는 50㎎/L kanamycin과 cefotaxim 300㎎/L을 포함하는 배지에서 선발하였다. PCR과 Southern hybridization분석에 의하여 형질전환체를 검증하였다.

• 한국정보과학회논문지:소프트웨어및응용
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• 제34권12호
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• pp.1056-1064
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• 2007

생체분자 컴퓨팅은 DNA와 같은 생체 분자를 이용하여 정보를 표현하고 처리하는 새로운 컴퓨팅 패러다임이다. 작은 부피에 존재하는 무수히 많은 분자와 화학 반응에 내재된 대규모 병렬성은 새로운 개념의 고성능 계산 기법에 영감을 주었고 이를 바탕으로 다양한 계산 모델 및 문제 해결을 위한 분자알고리즘이 개발되었다. 한편 생체 분자를 이용한 정보처리라는 특징은 생물학 문제에 적용될 수 있는 가능성을 시사한다. 유전자 발현 패턴과 같은 생화학적 분자 정보의 분석을 위한 도구로서의 가능성을 가지고 있는 것이다. 이러한 맥락에서 DNA 컴퓨팅 기반의 생체분자 퍼셉트론 모델이 제안되었고 그 실험적 구현 결과가 제시된 바 있다. 생체분자 퍼셉트론의 핵심인 가중치 표현 및 가중치-합 연산은 입력 분자와 가중치를 표현하는 프로브 분자간의 경쟁적 혼성화 반응에 기반하고 있다. 그러나 그 혼성화 반응에서 열역학적 대칭성을 가정하고 있기 때문에 사용하는 프로브에 따라 가중치 표현의 오차가 있을 수 있다. 본 논문에서는 비대칭적인 열역학적 특성을 고려하여 일반화된 혼성화 반응 모델을 제시하고, 이를 바탕으로 신뢰성 있는 생체 분자 퍼셉트론의 구현을 위한 가중치 코딩 방법을 제안한다. 그리고 본 논문에서 제시한 가중치 표현 방법의 정확성을 이전 모델과 컴퓨터 시뮬레이션을 통해 비교하고 한계 오차를 만족하기 위한 조건을 제시한다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제41회 하계 정기 학술대회 초록집
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• pp.108-108
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• 2011

Organometallic complexes containing unpaired spins, such as metalloporphyrin or metallophthalocyanine, have extensively studied with increasing interests of their promising model systems in spintronic applications. Additionally, the use of these complexes as an acceptor molecule in chemical sensors has recently received great attentions. In this presentation, we have investigated adsorption of nitric oxide (NO) molecules at Co-porphyrin molecules on Au(111) surfaces with scanning tunneling microscopy and spectroscopy at low temperature. At the location of Co atom in Co-porphyrin molecules, we could observe a Kondo resonance state near Fermi energy in density of states (DOS) before exposing NO molecules and the Kondo resonance state was disappeared after NO exposing because the electronic spin structure of Co-porphyrin were modified by forming a cobalt-NO bonding. Furthermore, we could locally control the chemical reaction of NO dissociations from NO-CoTPP by electron injections via STM probe. After dissociation of NO molecules, the Kondo resonance state was recovered in density of state. With a help of density functional theory (DFT) calculations, we could understand that the modified electronic structures for NO-Co-porphyrin could be occurred by metal-ligand hybridization and the dissociation mechanisms of NO can be explained in terms of the resonant tunneling process via molecular orbitals.

• Journal of Korean Neurosurgical Society
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• 제30권6호
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• pp.688-698
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• 2001

Objectives : Parkinson's disease is a well-known neurodegenerative disease characterized by dopaminergic cell death in the substantia nigra. The reactive gliosis by activated astrocytes and microglias is no more regarded as a simple sequel of neuronal cell death. Microglial activation takes place in a stereotypic pattern with graded morphologic and functional(resting, activated and phagocytic) changes. In Parkinson's disease animal model, the degree of microglial activation along the nigro-striatal dopaminergic tract has not been studied intensively. The purpose of this study was to elucidate the characteristics of microglial reaction and to grade its degree of activation at substantia nigra and corpus striatum using 6-hydroxydopamine induced rat model of Parkinson's disease. Methods : Using Sprague-Dawley rat, parkinsonian model was made by 6-hydroxydopamine(OHDA) induced destruction of medial and lateral substantia nigra(SN). The rat was sacrificed 3-, 5-, 7-, 14- and 21-day-after operation. For control group, we injected saline with same manner and sacrificed 3-day after operation. With immunohistochemistry, we examined dopaminergic neuronal cells and microglial expression using tyrosine hydroxylase (TH) and OX-42 antibodies, respectively. Also we performed in situ hybridization for osteopontin, a possible marker of subset in activated microglia. Results : 1) In lesioned side of substantia nigra and corpus striatum, the TH immunoreactivity was markedly decreased in whole experimental groups. 2) Using optical densitometry, microglia induced immunoreactivity of OX-42 was counted at SN and corpus striatum. At SN, it was increased significantly on the lesioned side in control and all time-dependent experimental groups. At striatum, it was increased significantly in post lesion 3-day group only(p <0.05). Compared to control group, immunoreactivity of OX-42 on lesioned side was increased in groups, except post lesion 21-day group, at SN. Only post lesion 3-day group showed significance at striatum(p <0.05). Compared to SN region, immunoreactivity of OX-42 was much weaker in striatum. 3) Microscopically, the microglias showed typically different activation pattern. At SN, numerous phagocytic microglias were found at pars compacta and reticularis of lesion side. At striatum, no phagocytic form was found and the intensity of staining was much weaker. 4) At SN, the immunoreactivity of osteopontin showed definite laterality and it was markedly increased at pars compacta of lesion side with relatively short duration time. At striatum, however, it was not detected by in situ hybridization technique. Conclusion : The nigral 6-OHDA induced rat model of Parkinson's disease revealed several characteristic patterns of microglial reaction. At SN, microglias was activated shortly after direct neuronal damage and maintained for about three weeks. In contrast, despite of sufficient dopaminergic insufficiency at striatum, activation of microglias was trivial, and distinguished 3 day later. Antegrade slow neuronal degeneration is major pathophysiology in striatal dopaminergic deficiency. So, the acuteness of neuronal damage and consequential degree of neuronal degeneration may be important factor for microglial activation in neurodegenerative diseases such as Parkinson's disease. Additionally, osteopontin may be a possible marker for several subsets of activated microglia, possibly the phagocytic form.

• 대한바이러스학회지
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• 제27권1호
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• pp.19-27
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• 1997

본 연구에서는 영장류에서 감염성 면역결핍 증상을 일으키는 type D simian retrovirus (SRV)를 검출하기 위해 SRV env 유전자의 특정 지역을 선정하여 증폭, 검색하는 중합효소 연쇄반응 (PCR)법을 개발하였다. 증폭반응의 대상부위인 SRV env 유전자의 3' 후반부는 서로 다른 3 종류의 SRV subtype 1, 2, 그리고 subtype 3에 걸쳐 높은 보존율을 보이고 있다. 반응 결과, 1차 PCR 만으로 3 종류의 SRV subtypes를 동시에 검출, 증폭하였으며 SRV와 더불어 영장류에서 감염성 면역결핍을 유도하는 주요 바이러스 simian immunodeficiency virus 또는 simian T-Iymphotropic virus type 1에 감염된 영장류의 peripheral blood mononuclear cells (PBMCs)을 비교, 완전한 증폭 특이성이 확인되었고 교차반응으로 인한 위양성반응은 발견되지 않았다. 한편, 위 증폭반응의 검출 민감도 측정을 위해 준정량적 적정 PCR을 수행하였으며 SRV 게놈과 증폭 대상 부위의 분자량을 기준으로 한 본 PCR법의 검출 한계는 단 한번의 증폭과 간단한 ethidium bromide 염색만으로 적어도 $5-7{\times}10^4$ 개의 PBMCs 중 한 개의 감염세포를 검출할 수 있는 것으로 확인되었다. 본 연구에서 확인된 신속성과 반응 특이성, 그리고 높은 민감도의 본 PCR 법은 현재 유일한 AIDS 연구모델인 영장류의 SIV 감염 연구 전후에 반드시 필요한 효과적인 SRV 감염검색에서 ELISA법의 위양성에 의한 약점을 보완하고 보다 높은 검출 민감도를 확보함으로써 연구모델 실험의 오류를 최소화하는 데 중요한 역할을 하게 될 것이다.