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RISS 인기검색어
- 검색키워드
- 저자 : Raeyeong Kim (검색결과 8 건)
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Kim, Raeyeong,Kanamaru, Shuji,Mikawa, Tsutomu,Pré,vost, Chantal,Ishii, Kentaro,Ito, Kentaro,Uchiyama, Susumu,Oda, Masayuki,Iwasaki, Hiroshi,Kim, Seog K,Takahashi, Masayuki Oxford University Press 2018 Nucleic acids research Vol.46 No.5
<P><B>Abstract</B></P><P>Mg<SUP>2+</SUP> ion stimulates the DNA strand exchange reaction catalyzed by RecA, a key step in homologous recombination. To elucidate the molecular mechanisms underlying the role of Mg<SUP>2+</SUP> and the strand exchange reaction itself, we investigated the interaction of RecA with Mg<SUP>2+</SUP> and sought to determine which step of the reaction is affected. Thermal stability, intrinsic fluorescence, and native mass spectrometric analyses of RecA revealed that RecA binds at least two Mg<SUP>2+</SUP> ions with K<SUB>D</SUB> ≈ 2 mM and 5 mM. Deletion of the C-terminal acidic tail of RecA made its thermal stability and fluorescence characteristics insensitive to Mg<SUP>2+</SUP> and similar to those of full-length RecA in the presence of saturating Mg<SUP>2+</SUP>. These observations, together with the results of a molecular dynamics simulation, support the idea that the acidic tail hampers the strand exchange reaction by interacting with other parts of RecA, and that binding of Mg<SUP>2+</SUP> to the tail prevents these interactions and releases RecA from inhibition. We observed that binding of the first Mg<SUP>2+</SUP> stimulated joint molecule formation, whereas binding of the second stimulated progression of the reaction. Thus, RecA is actively involved in the strand exchange step as well as bringing the two DNAs close to each other.</P>
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장윤정,Raeyeong Kim,Nataraj Chitrapriya,한성욱,김석규,배인호 대한화학회 2013 Bulletin of the Korean Chemical Society Vol.34 No.10
Direction of intercalation to DNA of the planar dipyrido[3,2-a:2',3'-c]phenazine ligands (dppz) of a bis-Ru(II) complex namely, [Ru(1,10-phenanthroline)2dipyrido[3,2-a:2',3'-c]phenazine]2+ linkered by a 1,3-bis(4- pyridyl)propane, was investigated by probing the behavior of 4',6-diamidino-2-phenylindole (DAPI) that bound deep in the minor groove. Bis-intercalation of DPPZ resulted in a little blue shift and hyperchromism in DAPI absorption band, and a large decrease in DAPI fluorescence intensity which accompined by an increase in the dppz emission intensity. Diminishing the intenisty of the positive induced circular dichroism (CD) and linear dichroism (LD) were also observed. These spectral changes indicated that insertion of dppz ligand caused the change of the binding mode of DAPI, which probably moved to the exterior of DNA from the minor groove and interacted with the phospghate groups of DNA by electrostatic interaction. At the surface of DNA, DAPI binds at the phosphate groups of DNA by electrostatic attraction. Consequently, this observation indicated that the dppz ligand intercalated from the minor groove.
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Chitrapriya, Nataraj,Kim, Raeyeong,Jang, Yoon Jung,Cho, Dae Won,Han, Sung Wook,Kim, Seog K. Korean Chemical Society 2013 Bulletin of the Korean Chemical Society Vol.34 No.7
The binding properties and sequence selectivities of ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ (bip = 4,4'-biphenylene (imidazo [4,4-f][1,10]phenanthroline) complexes with $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$ were investigated using conventional spectroscopic methods. When bound to $poly[d(A-T)_2]$, a large positive circular dichroism (CD) spectrum was induced in absorption region of the bridging moiety for both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes, which suggested that the bridging moiety sits in the minor groove of the polynucleotide. As luminescence intensity increased, decay times became longer and complexes were well-protected from the negatively charged iodide quencher compared to that in the absence of $poly[d(A-T)_2]$. These luminescence measurements indicated that Ru(II) enantiomers were in a less polar environment compared to that in water and supported by minor groove binding. An angle of $45^{\circ}$ between the molecular plane of the bridging moiety of the ${\Delta}{\Delta}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex and the local DNA helix axis calculated from reduced linear dichroism ($LD^r$) spectrum further supported the minor groove binding mode. In the case of ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex, this angle was $55^{\circ}$, suggesting a tilt of DNA stem near the binding site and bridging moiety sit in the minor groove of the $poly[d(A-T)_2]$. In contrast, neither ${\Delta}{\Delta}$-nor ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex produced significant CD or $LD^r$ signal in the absorption region of the bridging moiety. Luminescence measurements revealed that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes were partially accessible to the $I^-$ quencher. Furthermore, decay times became shorter when bis-Ru(II) complexes bound to $poly[d(G-C)_2]$. These observations suggest that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes bind at the surface of $poly[d(G-C)_2]$, probably electrostatically to phosphate group. The results indicate that ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ are able to discriminate between AT and GC base pairs.
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Nataraj Chitrapriya,Raeyeong Kim,장윤정,조대원,한성욱,김석규 대한화학회 2013 Bulletin of the Korean Chemical Society Vol.34 No.7
The binding properties and sequence selectivities of ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ (bip = 4,4'-biphenylene (imidazo [4,4-f][1,10]phenanthroline) complexes with poly[d(A-T)2] and poly[d(G-C)2] were investigated using conventional spectroscopic methods. When bound to poly[d(A-T)2], a large positive circular dichroism (CD) spectrum was induced in absorption region of the bridging moiety for both the ΔΔ- and ΛΛ-[μ- Ru2(phen)4(bip)]4+ complexes, which suggested that the bridging moiety sits in the minor groove of the polynucleotide. As luminescence intensity increased, decay times became longer and complexes were wellprotected from the negatively charged iodide quencher compared to that in the absence of poly[d(A-T)2]. These luminescence measurements indicated that Ru(II) enantiomers were in a less polar environment compared to that in water and supported by minor groove binding. An angle of 45° between the molecular plane of the bridging moiety of the ΔΔ-[μ-Ru2(phen)4(bip)]4+ complex and the local DNA helix axis calculated from reduced linear dichroism (LDr) spectrum further supported the minor groove binding mode. In the case of ΛΛ- [μ-Ru2(phen)4(bip)]4+ complex, this angle was 55°, suggesting a tilt of DNA stem near the binding site and bridging moiety sit in the minor groove of the poly[d(A-T)2]. In contrast, neither ΔΔ- nor ΛΛ-[μ-Ru2(phen)4- (bip)]4+ complex produced significant CD or LDr signal in the absorption region of the bridging moiety. Luminescence measurements revealed that both the ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ complexes were partially accessible to the I− quencher. Furthermore, decay times became shorter when bis-Ru(II) complexes bound to poly[d(G-C)2]. These observations suggest that both the ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ complexes bind at the surface of poly[d(G-C)2], probably electrostatically to phosphate group. The results indicate that ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ are able to discriminate between AT and GC base pairs.
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Won, A. Reum,Kim, Raeyeong,Jung, Maeng-Joon,Kim, Seog K.,Lee, Young-Ae Elsevier Sequoia [etc.] 2018 Inorganica chimica acta Vol.471 No.-
<P><B>Abstract</B></P> <P>The oxidative DNA cleavage induced by the [Cu(2,2′-bipyridine)<SUB>2</SUB>(NO<SUB>3</SUB>)]NO<SUB>3</SUB> (Cu(bpy)<SUB>2</SUB>) complex was examined using the linear dichroism (LD) technique. Using this method, the oxidative DNA cleavage by the Fenton mechanism was reported to occur through two sequential first-order reactions. As the Cu(bpy)<SUB>2</SUB> concentration increased, the rate constant of both first order reactions increased, as expected. The activation energy of the second step was estimated to be 0.190 kJ mol<SUP>−1</SUP>. A similar method was applied for various synthetic polynucleotides. Poly[d(G-C)<SUB>2</SUB>], poly(dG)·poly(dC), and poly(dA)·poly(dT) produced a time-dependent decrease in LD, which could be elucidated by a single component exponential decay. This observation is in contrast to Fenton-type oxidative DNA cleavage. On the other hand, poly[d(A-T)<SUB>2</SUB>] produced a time-dependent decrease in the LD magnitude, which could be elucidated by two sequential first order reactions.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Cu(bpy)<SUB>2</SUB> complex induced oxidative DNA cleavage. </LI> <LI> The cleavage rate constant for synthetic polynucleotides depended on the nature of base sequence. </LI> <LI> Poly[d(A-T)<SUB>2</SUB>] produced the mechanism similar to native DNA. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>Decrease in the LD magnitude at 260 nm for poly(dG)·poly(dC) (curve a), poly[d(G-C)<SUB>2</SUB>] (curve b), poly[d(A-T)<SUB>2</SUB>] (curve c), and poly(dA)·poly(dT) (curve d) at 20 °C.</P> <P>[DISPLAY OMISSION]</P>
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Jang, Yoon Jung,Kim, Raeyeong,Chitrapriya, Nataraj,Han, Sung Wook,Kim, Seog K.,Bae, Inho Korean Chemical Society 2013 Bulletin of the Korean Chemical Society Vol.34 No.10
Direction of intercalation to DNA of the planar dipyrido[3,2-a:2',3'-c]phenazine ligands (dppz) of a bis-Ru(II) complex namely, $[Ru(1,10-phenanthroline)_2dipyrido[3,2-a:2^{\prime},3^{\prime}-c]phenazine]^{2+}$ linkered by a 1,3-bis(4-pyridyl)propane, was investigated by probing the behavior of 4',6-diamidino-2-phenylindole (DAPI) that bound deep in the minor groove. Bis-intercalation of DPPZ resulted in a little blue shift and hyperchromism in DAPI absorption band, and a large decrease in DAPI fluorescence intensity which accompined by an increase in the dppz emission intensity. Diminishing the intenisty of the positive induced circular dichroism (CD) and linear dichroism (LD) were also observed. These spectral changes indicated that insertion of dppz ligand caused the change of the binding mode of DAPI, which probably moved to the exterior of DNA from the minor groove and interacted with the phospghate groups of DNA by electrostatic interaction. At the surface of DNA, DAPI binds at the phosphate groups of DNA by electrostatic attraction. Consequently, this observation indicated that the dppz ligand intercalated from the minor groove.
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