• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.206-206
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• 2006

Polymer induced turbulent drag reduction achieved by adding minute amounts of high molecular weight DNAs in aqueous solution was investigated using a rotating disk apparatus. The DNAs in this study include ${\lambda}-DNA$ and calf-thymus (CT) DNA. By putting emphasis on effect of CT-DNA concentration, its DR characteristics were compared with that of ${\lambda}-DNA$ possessing monodisperse molecular weight characteristics based on both DR efficiency and a mechanical degradation under turbulence. The DNA chains having much higher molecular size than that of ${\lambda}-DNA$ are observed to be more susceptible to mechanical degradation in a turbulent flow. This result was verified via electrophoresis. Furthermore, the coil to globule phase transition of DNA was also investigated under a turbulent flow.

• BMB Reports
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• v.34 no.6
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• pp.551-558
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• 2001

We extended the measurable time scale of DNA dynamics to submicrosecond using a long-lifetime metal-ligand complex, $[Ru(phen)_2(dppz)]^{2+}$ (phen=1,10-phenanthroline, dppz=dipyrido[3,2-a:2',3'-c]phenazine) (RuPD), which displays a mean lifetime near 350 ns. We partially characterized the fluorescence resonance energy transfer (FRET) in calf thymus DNA from RuPD to nile blue (NB) using frequency-domain fluorometry with a high-intensity, blue light-emitting diode (LED) as the modulated light source. There was a significant overlap of the emission spectrum of the donor RuPD with the absorption spectrum of the acceptor NB. The F$\ddot{o}$rster distance ($R_0$) that was calculated from the spectral overlap was $33.4\;{\AA}$. We observed dramatic decreases in the steady-state fluorescence intensities of RuPD when the NB concentration was increased. The intensity decays of RuPD were matched the closest by a triple exponential decay. The mean decay time of RuPD in the absence of the acceptor NB was 350.7 ns. In a concentration-dependent manner, RuPD showed rapid intensity decay times upon adding NB. The mean decay time decreased to 184.6 ns at $100\;{\mu}M$ NB. The FRET efficiency values that are calculated from the mean decay times increased from 0.107 at $20\;{\mu}M$ NB to 0.474 at $100\;{\mu}M$ NB concentration. The use of FRET with a long-lifetime metal-ligand complex donor is expected to offer the opportunity to increase the information about the structure and dynamics of nucleic acids.

• Archives of Pharmacal Research
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• v.25 no.2
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• pp.143-150
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• 2002

Fluorescent probes bound to DNA typically display nanosecond decay times and reveal only nanosecond motions. We extend the time range of measurable DNA dynamics using $[Ru(pby)_2(dppz)]^{2+}$ (bpy=2.2'-bipyridine, dppz=dipyrido[3,2-a2',3'-c]phenazine) (RuBD) which displays a mean lifetime near 90 ns. To test the usefulness of RuBD as a probe for diffusive processes in calf thymus DNA, we compared the efficiencies of fluorescence resonance energy transfer (FRET) using three donors which display lifetimes near 5 ns for acridine orange (AO), 22 ns for ethidum bromide (EB) and 92 ns for RuBD, with nile blue (NB) as the acceptor. The F rster distances for AO-NB, EB-NB and RuBD-NB donor-acceptor pairs were 42.3, 52.3, and $30.6{\;}{\AA}$, respectively. All three donors showed dramatic decreases in fluorescence intensities and more rapid intensity decays with increasing NB concentrations. The intensity decays of AO and EB in the presence of varying concentrations of NB were satisfactorily described by the one-dimensional FRET model without diffusion (Blumen and Manz, 1979). In the case of the long-lifetime donor RuBD, the experimental phase and modulation somewhat deviated from the recovered values computed from this model. The recovered NB concentrations and FRET efficiencies from the model were slightly larger than the expected values, however, the recovered and expected values did not show a significant difference. Thus, it is suggested that the lifetime of RuBD is too short to measure diffusive processes in calf thymus DNA.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2008.11a
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.1
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• pp.18-25
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• 2018

Replication protein A (RPA) is an essential single-stranded DNA binding protein in DNA processing. It is known that N terminal domain of RPA70 (RPA70N) recruits various protein partners including damage-response proteins such as p53, ATRIP, Rad9, and MRE11. Although the common binding residues of RPA70N were revealed, dynamic properties of the protein are not studied yet. In this study, we measured $^{15}N$ relaxation parameters ($T_1,\;T_2$ and heteronuclear NOE) of human RPA70N and analyzed them using model-free analysis. Our data showed that the two loops near the binding site experience fast time scale motion while the binding site does not. It suggests that the protein binding surface of RPA70N is mostly rigid for minimizing entropy cost of binding and the loops can experience conformational changes.

• BMB Reports
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• v.31 no.1
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• pp.89-94
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• 1998

The structures of the self-complementary decamer duplexes, $d(ACGTATACGT)_2$ (TATA-duplex) and $d(ACGTTAACGT)_2$, (TTAA-duplex) has been obtained in solution by proton NMR spectroscopy and restrained molecular dynamics. The duplexes are essentially B-type, with distortions apparent at the TATA and TTAA steps. Theses distortions and their effects on dynamics have been investigated by the measurement of imino proton exchange time of the base-pairs. The unusual opening kinetics of central A T base-pairs could be correlated to the abnormal structural properties of the corresponding sequences.

• BMB Reports
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• v.40 no.2
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• pp.135-141
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• 2007

Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.

• Korea-Australia Rheology Journal
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• v.20 no.3
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• pp.127-142
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• 2008

The development of fluorescence microscopy of single-molecule DNA in the last decade has fostered a bold jump in the understanding of polymer physics. With the recent advance of nanotechnology, devices with well-defined dimensions that are smaller than typical DNA molecules can be readily manufactured. The combination of these techniques has provided an unprecedented opportunity for researchers to examine confined polymer behavior, a topic far less understood than its counterpart. Here, we review the progress reported in recent studies that investigate confined polymer dynamics by means of single-molecule DNA experiments.

• Proceedings of the Korean Society of Potoscience Conference
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• 2005.06a
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• pp.29-29
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• 2005

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2203-2208
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• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.