• Title/Summary/Keyword: DNA molecules

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DNA Concentration Effect of Various Hydroxide Compounds on Stacking in Capillary Electrophoresis

  • Shin, Ah-Ram;Kang, Seong-Ho
    • Bulletin of the Korean Chemical Society
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    • v.32 no.12
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    • pp.4316-4320
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    • 2011
  • The effects of various hydroxide compounds on base stacking (BS) were investigated for pre-concentration of DNA molecules in capillary electrophoresis (CE). In BS, hydroxide ions ($OH^-$) were electrokinetically introduced after DNA sample injection. A neutralization reaction occurred between the $OH^-$ and $Tris^+$ of the running buffer, which resulted in a zone of lower conductivity. Within the low conductivity zone of the high electric field, the DNA molecules moved more rapidly and were concentrated in front of the low conductivity zone. At the same BS conditions of CE, the enhanced sensitivity of the DNA samples was dependent on the kind of multivalent cations in the hydroxide compounds. Except for LiOH, the hydroxide compounds with monovalent cations showed more effective BS than those with divalent cations because of solubility, ionic strength and electronegativity. The order of hydroxide compounds that enhance the detection sensitivity of DNA molecules was as follows: NaOH > $NH_4OH$ > KOH > $Ba(OH)_2$ > $Sr(OH)_2$ > LiOH > $Ca(OH)_2$ > $Mg(OH)_2$. $NH_4OH$, KOH and $Ba(OH)_2$ proved to be efficient hydroxide compounds to use as effective BS reagents in CE instead of NaOH.

Separation of large DNA molecules by pulsed field gel electrophoresis (역전장 전기영동장치를 이용한 대형 DNA 분리에 관한 연구)

  • Joo, Yi-seok;Casey, Thomas A;Yoon, Yong-dhuk
    • Korean Journal of Veterinary Research
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    • v.33 no.1
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    • pp.81-85
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    • 1993
  • Gel electrophoresis has proven to be one of the most useful of DNA separation and purification. The new technique of pulsed field gel electrophoresis (PFGE) is high resolution separation of large size DNA moleculs. Conventional continuous gel electrophresis can not be separation of large DNA fragments(20~50 k base). Field inversion gel electrophoresis(FIGE) is very useful for large DNA molecules. We have found that a pulse ratio ; 2 : 1, time ; 24hrs., volts ; $10^{volts}/_{cm}$, start ; 0.45sec, end ; 1sec, is most effectively resolves DNA fragment in the 6~50k base.

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Preparation and Atomic Force Microscopy (AFM) Characterization of DNA Scaffolds as a Template for Protein Immobilization

  • Kim, Hyeran;Lee, Hyun Uk;Lee, Jouhahn
    • Proceedings of the Korean Vacuum Society Conference
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    • 2014.02a
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    • pp.411.2-411.2
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    • 2014
  • The design of DNA nanostructures is of fundamental importance, the intrinsic value of DNA as a building-block material lies in its ability to organize other bio-molecules with nanometer-scale spacing. Here, we report the fabrication of DNA scaffolds with nano-pores (<10 nm size) that formed easily without the use of additives (i.e., avidin, biotin, polyamine, or inorganic materials) into large-scale structures by assembling DNA molecules at near room temperature ($30^{\circ}C$) and low pH (~5.5). Protein immobilization results also confirmed that a fibronectin (FN) proteins/large scale DNA scaffolds/aminopropylytriethoxysilane (APS)/SiO2/Si substrate with high sensitivity formed in a well-defined manner. The DNA scaffolds can be applied for use with DNA-based biochips, biophysics, and cell biology.

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Recent advances in developing molecular tools for targeted genome engineering of mammalian cells

  • Lim, Kwang-Il
    • BMB Reports
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    • v.48 no.1
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    • pp.6-12
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    • 2015
  • Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

Probe-based Charge Injection Study of DNA Charge Transfer for Applications to Molecular Electro-optic Switching (전극 기반의 전하 주입을 통한 DNA 전하수송 특성 측정)

  • Ryu, Ho-Jeong;Kim, Hee-Young;Kim, Dong-Hyun
    • 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.

Development of DNA Probe Assay System for Salmonella Species using Glass as substrate

  • Jeong, U-Seong;Lee, Ung-Hui;Baek, Se-Hwan
    • 한국생물공학회:학술대회논문집
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    • 2001.11a
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    • pp.235-236
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    • 2001
  • We developed a DNA probe analytical system with a patterned array of oligonucleotide molecules immobilized on glass surfaces. The detection capability of the system depended mainly on the way the capture probes were attached to the support as wen as the sequence. We optimized major variables to graft DNA molecules onto a glass support and the DNA probe assay was eventually accomplished without purification of the PCR product.

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RBF-POD reduced-order modeling of DNA molecules under stretching and bending

  • Lee, Chung-Hao;Chen, Jiun-Shyan
    • Interaction and multiscale mechanics
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    • v.6 no.4
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    • pp.395-409
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    • 2013
  • Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

Micromachined DNA Manipulation Device Using Circular Multi-Electrodes (원형 다중전극을 이용한 DNA 조작소자)

  • Moon, Sang-Jun;Yun, Jae-Young;Lee, Seung-S.;Nam, Hong-Kil;Chi, Yeun-Tae
    • Transactions of the Korean Society of Mechanical Engineers A
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    • v.27 no.7
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    • pp.1071-1075
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    • 2003
  • In this paper, we present a DNA manipulation device in the reaction chamber, which consists of a center electrode and circular outer electrodes of a reaction unit. The charged bio-molecules, DNA, are manipulated by the charge of the electrode in reaction unit. Controlling the induced dynamic electric field between the center electrode and the outer electrodes, concentration / repulsion / manipulation of bio-molecules are enabled at a periphery of electrode. Concentration of the fluorescent DNA at the center electrode is observed by applying +2V. Subsequently, applying -2V, the concentrated DNA is repelled rapidly from the center electrode, which makes dispersion completely in 0.5second. Furthermore, repeated applying +1V/-1V every 5 seconds at each outer electrode, we can circulate the DNA. We also investigate a micro-heater and sensor for DNA manipulation and reaction temperature. The coefficient of heat-resistance and heater temperature characteristic is 0.0043 and 100$^{\circ}C$/sec, respectively.

Immunoliposomes Carrying Plasmid DNA : Preparation and Characterization

  • Kim, Na-Hyung;Park, Hyo-Min;Chung, Soo-Yeon;Go, Eun-Jung;Lee , Hwa-Jeong
    • Archives of Pharmacal Research
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    • v.27 no.12
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    • pp.1263-1269
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    • 2004
  • The objective of this study was to characterize immunoliposomes carrying plasmid DNA with optimal encapsulation efficiency and antibody density. Plasmid DNA was encapsulated by the freezing/thawing method into liposomes composed of POPC (1-palmitoyl-2-oleoyl-sn-glycerol- 3-phosphocholine), DDAB (didodecyl dimethyl ammonium bromide), DSPE-PEG 2000 (distearoyl phosphatidyl ethanolamine polyethylene glycol 2000) and DSPE-PEG 2000-maleimide. The liposomes carrying plasmid DNA were extruded through two stacked polycarbonate filters, of different pore size, to control the liposome size. Then, rat IgG molecules were conjugated to the liposomes. The immunoliposomes containing plasmid DNA were separated from the free plasmid DNA and unconjugated IgG by Sepharose CL-4B column chromatography. The DNA amount encapsulated was affected by DDAB (cationic lipid) concentration, the initial amount of plasmid DNA between 10 ${\mu}g$ and 200 ${\mu}g$, the total lipid amount and plasmid DNA size, but not significantly by liposome size. By varying the ratio of DSPE-PEG 2000-maleimide to IgG, the number of IgG molecules per liposome was changed significantly.