• Title/Summary/Keyword: hybridization reaction model

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Detection and Analysis of DNA Hybridization Characteristics by using Thermodynamic Method (열역학법을 이용한 DNA hybridization 특성 검출 및 해석)

  • Kim, Do-Gyun;Gwon, Yeong-Su
    • The Transactions of the Korean Institute of Electrical Engineers C
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    • v.51 no.6
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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.

Simulation of DNA/DNA Hybridization Chain Reaction Using Thermodynamic Data (열역학적 데이터에 기반한 DNA/DNA 연쇄 결합 반응 시뮬레이션)

  • 장하영;신수용;장병탁
    • Proceedings of the Korean Information Science Society Conference
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    • 2003.10b
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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.

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A Simple and Efficient Subtractive Cloning Method

  • Min, Hyun-Jin;Park, Sang-Soo;Cho, Tae-Ju
    • BMB Reports
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    • v.34 no.1
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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.

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Analysis of Flavonoid 3',5'-Hydroxylase Gene in Transgenic Petunia (Petunia hybrida) Plants (형질 전환된 페튜니아 식물체에서의 Flavonoid 3',5' -Hydroxylase 유전자의 분석)

  • 김영희
    • Korean Journal of Plant Tissue Culture
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    • v.25 no.5
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    • pp.323-327
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    • 1998
  • The flavonoid biosynthetic pathway has been studied as a genetic model system, particularly in Petunia hybrida. In order to study the flavonoid biosynthetic pathway, we constructed a fusion gene system between Cauliflower Mosaic Virus (CaMV) 35S promoter and eggplant flavonoid 3', 5'-hydroxylase in pBI 121 plasmid. An optimal condition for plant regeneration was observed when internode explants were cultured on MS medium supplemented with IAA 0.2 mg/L plus BA 3 mg/L. For plant transformation internode explants of Petunia hybrida were precultured on BM medium supplemented with IAA 0.2 mg/L plus BA 3 mg/L. Putative transgenic plants were selected on medium containing kanamycin 50 mg/L plus cefotaxim 300 mg/L. Putative selected transformants were confirmed by amplification of selectable marker gene (nptII) by polymerase chain reaction (PCR) and Southern hybridization of flavonoid 3',5'-hydroxylase gene.

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Thermodynamics-Based Weight Encoding Methods for Improving Reliability of Biomolecular Perceptrons (생체분자 퍼셉트론의 신뢰성 향상을 위한 열역학 기반 가중치 코딩 방법)

  • Lim, Hee-Woong;Yoo, Suk-I.;Zhang, Byoung-Tak
    • Journal of KIISE:Software and Applications
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    • v.34 no.12
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    • pp.1056-1064
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    • 2007
  • Biomolecular computing is a new computing paradigm that uses biomolecules such as DNA for information representation and processing. The huge number of molecules in a small volume and the innate massive parallelism inspired a novel computation method, and various computation models and molecular algorithms were developed for problem solving. In the meantime, the use of biomolecules for information processing supports the possibility of DNA computing as an application for biological problems. It has the potential as an analysis tool for biochemical information such as gene expression patterns. In this context, a DNA computing-based model of a biomolecular perceptron has been proposed and the result of its experimental implementation was presented previously. The weight encoding and weighted sum operation, which are the main components of a biomolecular perceptron, are based on the competitive hybridization reactions between the input molecules and weight-encoding probe molecules. However, thermodynamic symmetry in the competitive hybridizations is assumed, so there can be some error in the weight representation depending on the probe species in use. Here we suggest a generalized model of hybridization reactions considering the asymmetric thermodynamics in competitive hybridizations and present a weight encoding method for the reliable implementation of a biomolecular perceptron based on this model. We compare the accuracy of our weight encoding method with that of the previous one via computer simulations and present the condition of probe composition to satisfy the error limit.

Adsorptions and Dissociations of Nitric Oxides at Metalloporphyrin Molecules on Metal Surfaces: Scanning Tunneling Microscopy and Spectroscopy Study

  • Kim, Ho-Won;Chung, Kyung-Hoon;Kahng, Se-Jong
    • Proceedings of the Korean Vacuum Society Conference
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    • 2011.08a
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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.

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Neuroglial Reaction in the Substantia Nigra and Striatum of 6-Hydroxydopamine Induced Parkinson's Disease Rat Model (흰쥐 흑질내 수산화도파민 주입으로 유도된 파킨슨병 모델에서 흑질과 선조체의 신경교세포 반응)

  • Yang, Kyung Won;Sung, Jae Hoon;Kim, Moon Chan;Lee, Moon Yong;Lee, Sang Won;Choi, Seung Jin;Park, Choon Keun;Kang, Joon Ki
    • Journal of Korean Neurosurgical Society
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    • v.30 no.6
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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.

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One-Stage Polymerase Chain Reaction for the Comprehensive Detection of Type D Retrovirus Provial DNA (Type D Retrovirus 감염의 포괄적 검색을 위한 One-Stage 중합효소 연쇄반응법의 개발)

  • Jeong, Yong-Seok
    • The Journal of Korean Society of Virology
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    • v.27 no.1
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    • pp.19-27
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    • 1997
  • To develop the polymerase chain reaction (PCR) for the detection of type D simian retrovirus (SRV) infection, an oligonucleotide primer pair was designed to hybridize to the sequences within env gene of SRV subtype 1 (SRV-1). The 3' proximal env sequences annealing to the primers had been rather conserved among three different subtypes of SRV, SRV-1, SRV-2, and SRV-3 (Mason-Pfizer Monkey Virus: MPMV). The PCR using the primer pair targeting an env region successfully detected and amplified all three subtypes of SRV with excellent specificity after single round of reaction. The tests with peripheral blood mononuclear cells infected either with simian immunodeficiency virus or simian T-Iymphotropic virus type 1, major immunosuppressive viral agents together with SRV in simian, verified the specificity of the PCR by excluding any cross reactivity. Semiquantitative titration PCR, amplifying serially diluted plasmid DNA of each subtype, was performed to evaluate sensitivity limits of the reaction. Based on molecular weight of each cloned SRV genome, the PCR should be able to detect one SRV-infected cell per more than $5-7{\times}10^4$ uninfected cells after simple ethidium bromide staining of resulting products. The PCR must be very efficient screening system with its quickness, certainty, and sensitivity for SRV-infected animals used in human AIDS research model. Second round amplification of the reaction products from the first PCR, or Southern hybridization by radiolabeled probes shall render to compete its efficacy to ELISA which has been the most sensitive technique to screen SRV infection but with frequent ambiguity problem.

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