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- Partial Differential equations, Calculus of Variations, Mathematical fluid dynamics
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- Graph Theory, Combinatorics, Combinatorial Optimization
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- 이기암
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- Analysis, Partial Differential Equations
- Office 1410
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- 이용남
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- Algebraic Geometry
- Office 1404-B
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- 차재춘
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- Geometric Topology
- Office 1410
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- Analysis, Hyperbolic Conservation Laws, Kinetic Theory
- Office 1410
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- Theoretical and Computational Biophysics
- Office 8214
- Tel 2660 / Fax 3820
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Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions Title : Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions Author : Hong, Seok-Cheol,Hyeon, Changbong Journal : JOURNAL OF PHYSICAL CHEMISTRY B, 2015
Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions NUMBER C17037 AUTHOR Hong, Seok-Cheol,Hyeon, Changbong TITLE Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions ARCHIVE FILE JOURNAL JOURNAL OF PHYSICAL CHEMISTRY B, 2015 ABSTRACT Single-molecule: FRET is One Of the most powerful and widely used biophysical techniques in biological sciences. It, however often suffers from limitations such as weak signal and limited measurement time intrinsic to single- Molecule fluorescence measurements. Despite several ameliorative measures taken to increase- measurement time, it is nearly impossible to acquire meaningful kinetic information on a molecule if conformational transitions of the molecule are ultraslow such that transition times ( (orig)) are. comparable to or longer than measurement times (delta t) limited by the finite lifetime of fluorescent dye. Here, to extract a reliable and accurate mean transition time from, a series of short time traces with ultraslow kinetics, we suggest seheme called sHaRPer (serialized Handshaking Repeated Permutation with end removal) that concatenates multiple time traces because data acquisition frequency f and measurement time (delta t) affect the estimation of mean transition time ( ), we provide Mathematical criteria that f, delta t, and should satisfy to make close enough to (orig) Although application of the sHaRPer: methods a potential risk of distorting the time,constants of individual kinetic phases if the data are described with kinetic partitioning, We, also provide criteria to avoid such distortion. Our sHaRPer method is a useful way to handle single-molecule data:With,slow transition kinetics This,study:provides a practical vide to use sHaRPer.
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Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation Title : Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation Author : Hong, Seok-Cheol,Hyeon, Changbong Journal : JOURNAL OF PHYSICAL CHEMISTRY B, 2014
Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation NUMBER C15010 AUTHOR Hong, Seok-Cheol,Hyeon, Changbong TITLE Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation ARCHIVE FILE JOURNAL JOURNAL OF PHYSICAL CHEMISTRY B, 2014 ABSTRACT Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li+-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li+. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs.
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Direct observation of the formation of DNA triplexes by single-molecule FRET measurements Title : Direct observation of the formation of DNA triplexes by single-molecule FRET measurements Author : Hong, Seok-Cheol Journal : CURRENT APPLIED PHYSICS, 2012
Direct observation of the formation of DNA triplexes by single-molecule FRET measurements NUMBER null AUTHOR Hong, Seok-Cheol TITLE Direct observation of the formation of DNA triplexes by single-molecule FRET measurements ARCHIVE FILE JOURNAL CURRENT APPLIED PHYSICS, 2012 ABSTRACT In this report we investigated the effects of various biological and chemical factors (DNA sequence, pH, ions, and molecularity) on the formation of DNA triplexes through single-molecule FRET technique. Using this method, we determined how the third strand bound to a DNA duplex and how stable the triplex structure was under various conditions. From this study, we not only verified a variety of well-known features of DNA triplex but also discovered or experimentally supported several interesting behaviors: at neutral pH, a pyrimidine-motif triplex can be formed; the parallel arrangement was not only possible but also dominant over the antiparallel arrangement for a purine-motif triplex. We demonstrated that our method is a versatile analytical tool in studying structural aspects of nucleic acids, particularly non-classical DNA structures, and provides insights into physical mechanism of such structures. (C) 2012 Elsevier B. V. All rights reserved.
- 정형채
- KIAS Visiting Professor
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