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Energetics of Z-DNA Binding Protein-Mediated Helicity Reversals in DNA, RNA, and DNA–RNA Duplexes
Bae, Sangsu,Kim, Yuyoung,Kim, Doyoun,Kim, Kyeong Kyu,Kim, Yang-Gyun,Hohng, Sungchul American Chemical Society 2013 The journal of physical chemistry. B, Condensed ma Vol.117 No.44
<P>Z-DNA binding proteins (ZBPs) specifically recognize and stabilize left-handed double helices, including Z-DNA and Z-RNA. However, the energetics of Z-form stabilization by ZBPs have never been characterized due to the technical limitations of bulk studies, resulting in an unclear understanding of the ZBP operational mechanism at the molecular level. Here, we use single-molecule fluorescence resonance energy transfer (FRET) to determine the energetics of Z-form stabilization by ZBP for DNA, RNA, and DNA–RNA duplexes, revealing that the formation of B–Z or A–Z junctions dominates the thermodynamics and kinetics of Z-form stabilization. Furthermore, in contrast to general assumptions, the Z-form is most efficiently and most rapidly formed in the DNA–RNA hybrid duplex due to the greatly reduced junction energy in the DNA–RNA hybrid.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2013/jpcbfk.2013.117.issue-44/jp409862j/production/images/medium/jp-2013-09862j_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp409862j'>ACS Electronic Supporting Info</A></P>
Z-DNA stabilization is dominated by the Hofmeister effect
Bae, Sangsu,Son, Heyjin,Kim, Yang-Gyun,Hohng, Sungchul The Royal Society of Chemistry 2013 Physical chemistry chemical physics Vol.15 No.38
<P>The manner in which Z-DNA is stabilized at high salt concentrations remains unclear. Here, we systematically examine the Z-DNA-stabilizing capabilities of different salts. The strong correlation between the double-stranded DNA denaturation and B-to-Z transition efficiencies indicates that Z-DNA is mainly stabilized by the Hofmeister effect.</P> <P>Graphic Abstract</P><P>Z-DNA is stabilized mainly by the Hofmeister effect of salts rather than by the electrostatic screening effects of salts. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3cp52047a'> </P>
Bae, Sangsu,Park, Jeongbin,Kim, Jin-Soo Oxford University Press 2014 Bioinformatics Vol.30 No.10
<P><B>Summary:</B> The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted manner. CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) enable genome editing in cultured cells, animals and plants, but are limited by off-target mutations. Here, we present a novel algorithm termed Cas-OFFinder that searches for potential off-target sites in a given genome or user-defined sequences. Unlike other algorithms currently available for identification of RGEN off-target sites, Cas-OFFinder is not limited by the number of mismatches and allows variations in protospacer-adjacent motif sequences recognized by Cas9, the essential protein component in RGENs. Cas-OFFinder is available as a command-line program or accessible via our website.</P><P><B>Availability and implementation:</B> Cas-OFFinder free access at http://www.rgenome.net/cas-offinder.</P><P><B>Contact:</B>baesau@snu.ac.kr or jskim01@snu.ac.kr</P>
Quantum-Structure-Dependent Excitonic Carrier Dynamics of InxGa1-xN/GaN Multi-Quantum-Wells
Sangsu Hong,Alexander Fomin,Bae Kyun Kim,Gyu Han Lee,조형균,Je Won Kim,June Sik Park,주태하,Yong Seok Kim,Young Joon Yoon 한국물리학회 2007 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.50 No.6
The excitonic carrier dynamics taking place in In$_x$Ga$_{1-x}$N/GaN multi-quantum-well systems have been studied by using low temperature picosecond-time-resolved photoluminescence (LT-TRPL), high resolution transmission electron microscopy (HR-TEM), X-ray photoelectron spectroscopy (XPS), Dynamic time of flight secondary ion mass spectrometry (TOF-SIMS), and quantum mechanical simulation methods. Both time-integrated and time-resolved photoluminescence spectra of In$_x$Ga$_{1-x}$N/GaN multi-quantum-wells with different well thicknesses and indium compositions were measured at 10 K. We assigned the natural radiative lifetime of each sample from the time-resolved PL. We observed that the natural radiative lifetime of In In$_x$Ga$_{1-x}$N/GaN multi-quantum-wells depended strongly on the well thickness and the indium composition. To support the measured natural radiative lifetimes, we calculated the excitonic oscillator strengths of the In$_x$Ga$_{1-x}$N/GaN multi-quantum-wells as functions of well thickness and indium composition by using a 2-D particle-in-a-box model. Values of the well thicknesses and indium compositions from the HR-TEM and XPS compositional depth profiling were used to achieve more realistic computational results and to corroborate the measured natural radiative lifetimes of In$_x$Ga$_{1-x}$N/GaN multi-quantum wells.
이상수(Sangsu Lee),박용배(Yong Bae Park) 한국전자파학회 2017 한국전자파학회논문지 Vol.28 No.9
본 논문에서는 SMA 커넥터를 이용한 3축 펄스 탐지기의 동작 특성을 분석한다. 상용 시뮬레이터를 이용하여 3축 펄스탐지기를 모델링하고, 펄스가 인가됐을 때 동작 특성을 확인 및 분석하여 펄스 탐지기로써의 응용이 가능함을 확인한다 In this paper, the performance characteristic of 3 dimensional pulse detector using SMA connector is analyzed. Modeling of 3D pulse detectors is done in a commercial simulator. When a pulse is incident on the detector, we analyze the performance characteristics of the detector and verify the feasibility of the pulse detector.
Analysis of a Tapered Rectangular Waveguide for V to W Millimeter Wavebands
Yong Bae Park,Jae-Yong Kwon,Dongchan Son,Sangsu Lee 한국전자파학회JEES 2018 Journal of Electromagnetic Engineering and Science Vol.18 No.4
An electromagnetic boundary-value problem of a tapered rectangular waveguide is rigorously solved based on eigenfunction expansion and the mode-matching method. Scattering parameters of the tapered rectangular waveguide are represented in a series form and calculated in terms of different rectangular waveguide combinations. Computation is performed to analyze reflection and transmission characteristics. Conductor loss by surface current density is also calculated and discussed.
Nanoscale RRAM-based synaptic electronics: toward a neuromorphic computing device
Park, Sangsu,Noh, Jinwoo,Choo, Myung-lae,Sheri, Ahmad Muqeem,Chang, Man,Kim, Young-Bae,Kim, Chang Jung,Jeon, Moongu,Lee, Byung-Geun,Lee, Byoung Hun,Hwang, Hyunsang IOP Pub 2013 Nanotechnology Vol.24 No.38
<P>Efforts to develop scalable learning algorithms for implementation of networks of spiking neurons in silicon have been hindered by the considerable footprints of learning circuits, which grow as the number of synapses increases. Recent developments in nanotechnologies provide an extremely compact device with low-power consumption.</P><P>In particular, nanoscale resistive switching devices (resistive random-access memory (RRAM)) are regarded as a promising solution for implementation of biological synapses due to their nanoscale dimensions, capacity to store multiple bits and the low energy required to operate distinct states. In this paper, we report the fabrication, modeling and implementation of nanoscale RRAM with multi-level storage capability for an electronic synapse device. In addition, we first experimentally demonstrate the learning capabilities and predictable performance by a neuromorphic circuit composed of a nanoscale 1 kbit RRAM cross-point array of synapses and complementary metal–oxide–semiconductor neuron circuits. These developments open up possibilities for the development of ubiquitous ultra-dense, ultra-low-power cognitive computers.</P>