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Kim, Sung Hyun,Kim, So Young,Jung, Kwang-Hwan,Kim, Doseok Japan Society for Bioscience, Biotechnology, and A 2015 Bioscience, Biotechnology, and Biochemistry Vol.79 No.7
<P>Anabaena sensory rhodopsin transducer (ASRT) is believed to be a major player in the photo-signal transduction cascade, which is triggered by Anabaena sensory rhodopsin. Here, we characterized DNA binding activity of ASRT probed by using fluorescence correlation spectroscopy. We observed clear decrease of diffusion coefficient of DNA upon binding of ASRT. The dissociation constant, K(D), of ASRT to 20?bp-long DNA fragments lied in micro-molar range and varied moderately with DNA sequence. Our results suggest that ASRT may interact with several different regions of DNA with different binding affinity for global regulation of several genes that need to be activated depending on the light illumination.</P>
Molecular mechanism of sequence-dependent stability of RecA filament
Kim, Sung Hyun,Joo, Chirlmin,Ha, Taekjip,Kim, Doseok Oxford University Press 2013 Nucleic acids research Vol.41 No.16
<P>RecA is a DNA-dependent ATPase and mediates homologous recombination by first forming a filament on a single-stranded (ss) DNA. RecA binds preferentially to TGG repeat sequence, which resembles the recombination hot spot Chi (5′-GCTGGTGG-3′) and is the most frequent pattern (GTG) of the codon usage in <I>Escherichia coli</I>. Because of the highly dynamic nature of RecA filament formation, which consists of filament nucleation, growth and shrinkage, we need experimental approaches that can resolve each of these processes separately to gain detailed insights into the molecular mechanism of sequence preference. By using a single-molecule fluorescence assay, we examined the effect of sequence on individual stages of nucleation, monomer binding and dissociation. We found that RecA does not recognize the Chi sequence as a nucleation site. In contrast, we observed that it is the reduced monomer dissociation that mainly determines the high filament stability on TGG repeats. This sequence dependence of monomer dissociation is well-correlated with that of ATP hydrolysis, suggesting that DNA sequence dictates filament stability through modulation of ATP hydrolysis.</P>
Park, Dong Hyuk,Jeong, Mi-Yun,Kim, Mikyung,Cho, Eun Hei,Kim, Dae-Chul,Song, Hugeun,Kim, Jeongyong,Shim, Tae Kyu,Kim, Doseok,Joo, Jinsoo American Scientific Publishers 2009 Journal of Nanoscience and Nanotechnology Vol.9 No.5
<P>The enhanced nanometer-scale photoluminescence (PL) and quantum yield of hybrid double layered nanotubes (HDLNTs) consisting of a light-emitting poly(3-methylthiophene) (P3MT) nanotube coated with nanometer-scale copper (Cu) metal were observed and presented. The HDLNTs of the Cu coated P3MT (P3MT/Cu) were synthesized through a sequential electrochemical synthetic method in an anodic alumina oxide (Al2O3) nanoporous template. We confirmed that the Cu nanotubes were covered outside the light emitting P3MT nanotubes based a high resolution transmission electron microscope image. From laser confocal microscope (LCM) PL experiments of an isolated single strand of the P3MT nanotubes and of their HDLNTs, we observed a -100 times enhancement of the PL peak intensity for the HDLNTs of P3MT/Cu compared to that of the P3MT single nanotube, which was qualitatively confirmed through the measurement of the quantum yield. The energy and/or charge transfer effects in surface plasmon resonance contributed to the larger enhancement of the PL efficiency of the hybrid P3MT/Cu nanotubes. The PL decay life-time of the excitons of the P3MT nanotubes using a time resolved PL was not changed after the formation of the HDLNTs, implying that the PL enhancement of the hybrid nanotubes might have originated from fluorescence, not phosphorescence.</P>
Photoluminescence Characteristics of Merocyanine Dyes in Ionic Liquids
심태규,Doseok Kim,H. H. Yoon,김현성,Jaeho Sung,Kyungbyung Yoon,Yukio Ouchi 한국물리학회 2006 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.48 No.6
The photoluminescence (PL) characteristics of merocyanine dye molecules in ionic liquids of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM]PF6) and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF4) with different purity grades were investigated. The absorption spectra for this dye in all the ionic liquid solvents investigated looked very similar while the PL emission spectra differed markedly depending on the type of ionic liquid and the impurity content. In all purity grades of [BMIM]BF4 and the ultrahigh grade of [BMIM]PF6, the PL spectra of these merocyanine solutions showed a single peak around 480 nm. However, when a lower grade of [BMIM]PF6 was used as the solvent, an additional PL peak appeared around 575 nm. The deprotonation from the hydroxyl group of the merocyanine molecule after photoexcitation is proposed to explain the phenomenon in this unique solvent system.n
Ao, Mingqi,Kim, Doseok American Chemical Society 2013 Journal of chemical and engineering data Vol.58 No.6
<P>The interfacial and bulk properties of the aqueous solutions of imidazolium-based ionic liquids with different halide anions ([C<SUB>12</SUB>mim]Cl, [C<SUB>12</SUB>mim]Br, [C<SUB>12</SUB>mim]I) were investigated by surface tension and electrical conductivity measurements. The lowest surface tension (γ<SUB>cmc</SUB>) and maximum surface excess concentration (Γ<SUB>max</SUB>) values from the surface tension measurements showed that [C<SUB>12</SUB>mim]I had the highest surface activity. The thermodynamic pontentials of micellization (Δ<I>G</I><SUP>0</SUP><SUB>m</SUB>, Δ<I>H</I><SUP>0</SUP><SUB>m</SUB>, Δ<I>S</I><SUP>0</SUP><SUB>m</SUB>) indicated that the micellization of [C<SUB>12</SUB>mim]Cl and [C<SUB>12</SUB>mim]Br was entropy-driven, while that of [C<SUB>12</SUB>mim]I was enthalpy-driven at 15 °C but entropy-driven above 20 °C. This distinct behavior for [C<SUB>12</SUB>mim]I was thought to be due to the higher binding affinity of I<SUP>–</SUP> to the micellar interface.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jceaax/2013/jceaax.2013.58.issue-6/je301147k/production/images/medium/je-2012-01147k_0003.gif'></P>
Anion exchange in ionic liquid mixtures
Cha, Seoncheol,Kim, Doseok The Royal Society of Chemistry 2015 Physical chemistry chemical physics Vol.17 No.44
<P>Advantage of ionic liquids as designer solvents can be maximized by mixing different ionic liquids (ILs) for a possibility of continuous tunability of material properties. The property of these mixed ILs would be determined by their microscopic conformation between cations and anions. The mixtures of two ILs having 1-butyl-3-methylimidaolium cations and different anions were investigated by IR and NMR spectroscopy, utilizing that the vibrational frequencies of the C–H stretching and bending modes of the most acidic proton in the imidazolium ring of the cation and the NMR chemical shift for the corresponding proton were clearly distinct between the ILs having different anions. The IR absorption spectra of the IL mixtures at different concentrations were well-matched to weighted sums of the two spectra of the pure ILs. In contrast, the two distinct peaks in the NMR spectra of the pure ILs coalesced into a single peak, which shifted continuously following the relative portion of two different ILs in the mixture. IR spectroscopy in the optical frequency range seems to take the instantaneous snapshot of the cation–anion interaction, while NMR spectroscopy in the radio-frequency (∼500 MHz) range samples over a much longer timescale, enough for the cation to interact with different anion species in the mixture.</P> <P>Graphic Abstract</P><P>Anion exchange in ionic liquid mixtures measured by IR and NMR spectroscopy. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c5cp04276c'> </P>
Density Profiles of Liquid/Vapor Interfaces Away from Their Critical Points
Bu, Wei,Kim, Doseok,Vaknin, David American Chemical Society 2014 JOURNAL OF PHYSICAL CHEMISTRY C - Vol.118 No.23
<P>We examine the applicability of various model profiles for the liquid/vapor interface by X-ray reflectivities on water and ethanol and their mixtures at room temperature. Analysis of the X-ray reflecivities using various density profiles shows an error-function like profile is the most adequate within experimental error. Our findings, together with recent observations from simulation studies on liquid surfaces, strongly suggest that the capillary-wave dynamics shapes the interfacial density profile in terms of the error function.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpccck/2014/jpccck.2014.118.issue-23/jp504374z/production/images/medium/jp-2014-04374z_0006.gif'></P>