Showing papers by "Seog K. Kim published in 2012"
TL;DR: In this article, solvent chirality transfer was examined using conjugated polymer with intramolecular stack structure (IaSS), and it was shown that axial chirability was significantly affected by the chain length and substitution position of the side alkyl groups.
Abstract: Solvent-to-polymer chirality transfer was examined using conjugated polymer with intramolecular stack structure (IaSS). When achiral poly(diphenylacetylene)s (PDPAs) dissolved in limonene, the solvent chirality was successfully transferred to the side phenyl stack structure, leading to intramolecular axial chirality. The phenyl–phenyl IaSS was under thermodynamic control to readily undergo asymmetric changes in chiral limonene, leading to optical activity in the isotropic structure between the main chain and resonant side phenyl rings. The axial chirality was significantly affected by the chain length and substitution position of the side alkyl groups. The longer alkyl chains and bulkier alkyl group prevented direct intermolecular interactions between the side phenyl rings and the chiral limonene molecules. PDPA with sterically congested, highly stable, and regulated IaSS was not favorable for efficient solvent-to-polymer chirality transfer.
96 citations
TL;DR: Strong overlap between emission spectrum of ethidium and the absorption spectrum of porphyrins when they simultaneously bound to DNA was found suggesting the mechanism behind energy transfer is, at least in part, the Förster type resonance energy transfer (FRET).
Abstract: Binding geometry to DNA and the efficiency as a donor for energy transfer of various metallo- and nonmetallo-porphyrins were investigated mainly by polarized light spectrscopy and fluorescence measurements. Planar porphyrins including nonmetallo meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP), CuTMPyP, and NiTMPyP produced large red-shift and hypochromism in absorption spectrum and a negative circular dichroism (CD) in the Soret band suggesting that these porphyrins intercalate between DNA base-pairs as expected. In the intercalation pocket, the molecular plane of these porphyrins tilts to a large extent. From a linear dichroism (LD) study, the angle between the two electric transition moments in the Soret band were 16°, 12°, and 11° for TMPyP, NiTMPyP, and CuTMPyP, respectively. On the other hand, porphyrins with axial ligands namely, VOTMPyP, TiOTMPyP, and CoTMPyP, produced a positive CD signal in the Soret band. Hyperchromism and less red-shift were apparent in the absorption spectrum. These ob...
23 citations
TL;DR: Coupling can occur between the porphyrins when they are separated at least two DNA base-pairs according to the nearest neighboring site exclusion model and this coupling interaction was the weakest for NiTMPyP.
Abstract: The binding modes of cationic porphyrins, namely M-meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (MTMPyP, where M = free base, Cu(II), Ni(II), Co(III), Mn(III), V(IV)═O, and Ti(IV)═O), to native ...
21 citations
TL;DR: From these observations, a conceivable binding mode of ZnTMPyP to Z-form poly[d(G-C)(2)] complex was proposed, in which Zn tiptrakis(N-methylpyridinium-4-yl)porphyrin binds at the major groove or across the groove.
Abstract: Zn(II) meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (ZnTMPyP) produced a unique linear dichroism (LD) spectrum when forming a complex with Z-form poly[d(G-C)2]. The spectrum was characterized by a large positive wavelength-dependent LD signal in the Soret absorption region. The magnitudes of LD in both the DNA and Soret band increased as the [porphyrin]/[DNA base] ratio increased and were larger by 20–40 times compared to the negative LD of the ZnTMPyP bound to B-form poly[d(G-C)2] and poly[d(A-T)2]. The angles calculated from LD were respectively 49° and 42° for Bx and By transitions of the porphyrin with respect to the local helix axis of Z-form poly[d(G-C)2]. The appearance of the unique LD spectrum for the Z-form poly[d(G-C)2] complex was accompanied by a bisignate circular dichroism spectrum in the Soret region, whose magnitude was proportional to the square of the porphyrin concentration, suggesting a stacking interaction between Z-form poly[d(G-C)2]-bound ZnTMPyP with other bound ZnTMPyP. From t...
12 citations
TL;DR: Lower linear dichroism spectroscopy showed angles of o-CuTMPyP's electric transition moments, in which the periphery pyridinium ring was prevented from free rotation, of 59° and 61° with respect to the local DNA helix axis, indicating that hydroxyl radicals and singlet oxygen were likely reactive species responsible for the cleavage.
Abstract: The photo-induced cleavage of pGEM-7zf-NIS super-coiled DNA by Cu(II)-meso-tetrakis(n-N-methylpyridiniumyl)porphyrins (n = 2, 3, 4 referred to as o-, m- and p-CuTMPyP, respectively) and their binding mode were investigated in this study. m-CuTMPyP was most efficient in cleavage than o- and p-CuTMPyP isomers. Cleavage was suppressed by N2 bubbling, suggesting that the cleavage occurred by an oxidative cleavage mechanism. Sodium azide, an 1O2 quencher, and DMSO, a hydroxyl radical scavenger, inhibited cleavage, indicating that hydroxyl radicals and singlet oxygen were likely reactive species responsible for the cleavage. Reduced linear dichroism spectroscopy showed angles of o-CuTMPyP's electric transition moments, in which the periphery pyridinium ring was prevented from free rotation, of 59° and 61° with respect to the local DNA helix axis. The spectra of m- and p-CuTMPyP complexed with pGEM-7zf-NIS DNA were characterized by large signals in the Soret band, coincident with those of known intercalated porphyrins.
8 citations
TL;DR: Different pulse voltammogram in the presence of ctDNA suggest that iron ions are recyclable at acidic pH, whereas they may form an electrically stable complex with DNA at high pH condition.
Abstract: addition to phosphate buffer induced significant change in the redox cycle of iron, indicating that iron may bind DNA as a complex with phosphate. Different pulse voltammogram in the presence of ctDNA suggest that iron ions are recyclable at acidic pH, whereas they may form an electrically stable complex with DNA at high pH condition.
3 citations
TL;DR: In this paper, the binding mode of a porphyrin dimer to double stranded native DNA was investigated using normal electric absorption, circular dichroism (CD) and linear dichroisms (LD) spectroscopies.
Abstract: The binding mode of a porphyrin dimer to double stranded native DNA was investigated in this study using normal electric absorption, circular dichroism (CD) and linear dichroism (LD) spectroscopies. At the time of mixing, the spectral properties of the porphyrin dimer upon its association with DNA were characterized by hypochromism and a red shift in the absorption spectrum and by complicated CD and negative LD in the Soret region. As time elapsed, the CD spectrum became a negative single band and the negative LD signal increased. These spectral changes suggested that the majority of both porphyrin moieties of the dimer intercalated between the DNA base-pairs. The changes in the spectral characteristics of the DNA bound porphyrin-dimer were similar when the minor groove of DNA was saturated by 4′,6-diamidino-2-phenylindole (DAPI), which is well-known minor groove binding molecule. The spectral properties of DAPI, which can be summarized by a large positive induced CD in the DAPI absorption region (300~400 nm) and wavelength-independent positive reduced LD, remained intact when the porphyrin dimer was present. These observations indicated that both DAPI and porphyrin bind to DNA simultaneously, and furthermore, the bis-intercalation of the porphyrin dimer occurs in the major groove.
1 citations
TL;DR: In this article, the slow intercalation of the second porphyrin moiety of poly[d(G-C)2] was investigated by normal absorption and circular dichroism spectroscopy.
Abstract: One of the porphyrin moieties of the porphyrin dimer intercalates rapidly between the DNA base-pairs, followed by the slow intercalation of the other. The slow intercalation of the second porphyrin moiety of porphyrin dimer to poly[d(G-C)2] was investigated by normal absorption and circular dichroism spectroscopy. The change in absorbance in the Soret band of porphyrin upon association with poly[d(G-C)2] can be best elucidated by the combination of the two single exponential curves, suggesting the intercalation occurred via two independent first order reactions. Activation energies of these two first order reactions were calculated to be 0.37 kcal/mol and 3.19 kcal/mol, respectively. The intercalation associated with lower activation energy can be assigned to the intercalation of second porphyrin moiety to 5′CG3′ site while that with higher activation energy to 5′GC3′ intercalation site. Increasing the flexibility of poly[d(G-C)2] by adding Na+ ion resulted in an enhancement of the reaction rate for both steps in an exponential manner.
1 citations