Showing papers by "Seog K. Kim published in 2010"

Conformational analysis of genotoxic benzo[a]pyrene- 7,8-dione-duplex DNA adducts using a molecular dynamics method.

Abstract: Benzo[a]pyrene-7,8-quinone (BPQ), a metabolite of the wide spread carcinogen benzo[a] pyrene, has been known to form adducts with DNA bases, namely guanine and adenine. The adducts include stereoisomers of the eight BPQ-G1,2 and products of the formation of the cyclic five-member ring between BPQ and the G base. The stereochemical characteristics, structural properties, and thermodynamic aspects of the formation of the BPQ-G modified duplexes were investigated in this work using molecular modeling and a molecular dynamics (MD) simulation technique. Three conformations for the BPQ- oligonucleotides adduct showed the most favorable free energy (AG). The molecular plane of the BPQ is nearly perpendicular to the DNA base plane for all three stable adducts. In two adducts, BPQ is located in the minor groove with either anti or syn conformations around the glycosidic bond. One of adducts in which BPQ locates into the major groove with the anti conformation around the glycosidic bond was also energetica...

Synthesis and characterization of enantiopure copper(II) complexes using chiral bidentate ligands

Abstract: Chiral copper(II) complexes of the types [CuII(R/S-ppme)3](ClO4)2 and [CuII(R/S-ppme)2(SO4)] have been synthesized by reactions of Cu(ClO4)2·6H2O and CuSO4·5H2O with R/S-ppme in methanol under aerobic conditions (R/S-ppme = (R/S)-(±)-1-phenyl-N-(pyridine-2-ylmethylene)ethanamine). All complexes were isolated and characterized by X-ray crystallography and circular dichroism (CD): (Λ)-[CuII(R-ppme)3](ClO4)2 (1), (Δ)-[Cu(S-ppme)3](ClO4)2·H2O (2), (Δ)-[CuII(R-ppme)2(SO4)]·4CH3OH (3), and (Λ)-[CuII(S-ppme)2(SO4)]·4CH3OH (4). 1 and 2 with ClO4− anions are formed as tris(R/S-ppme) copper(II) complexes, while 3 and 4 with SO42− are formed as bis(R/S-ppme) copper(II) complexes. The structures of 1 with R-ppmes and 4 with S-ppmes show the same absolute configurations (Λ). In contrast, 2 with S-ppmes and 3 with R-ppmes exhibit Δ configurations. In the electron paramagnetic resonance (EPR) spectra of 1 and 3, both compounds demonstrate z-axis elongated structures. The CD spectra of 1 and 2 show Cotton effects in an enantiomeric pattern; those of 3 and 4 also display the same effects.

Effect of number and position of positive charges on the stacking of porphyrins along poly[d(A-T)(2)] at high binding densities.

Abstract: At high porphyrin densities, the effects of the number and position of the positive charges of the periphery ring on the stacking of the porphyrin on poly[d(A-T)2] was investigated using polarized spectroscopy, including circular and linear dichroism (CD and LD, respectively). The CD spectrum of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin(TMPyP) consisted of two positive bands in the Soret absorption region at low [porphyrin]/[DNA base] ratios (R ratios) and changed to two distinguishable categories of the bisignate CD spectrum with increasing R ratio. These CD spectra were attributed to the monomeric groove binding, and the moderately and extensively stacked TMPyPs. In contrast, trans-bis(N-methylpyridinium-4-yl)porphyrin (trans-BMPyP) dominantly produced a CD spectrum that corresponded to the extensive stacking, except at the lowest R ratio that was used in this work (R = 0.04). However, for cis-bis(N-methylpyridinium-4-yl)porphyrin (cis-BMPyP), the intensity of the apparent bisignate CD signal was ...

Binding Modes of New Bis-Ru(II) Complexes to DNA: Effect of the Length of the Linker

Abstract: complexes (bis-Ru(II) complexes) tethered by lin-kers of various lengths were synthesized and their binding properties to DNA investigated by normal absorption and linear dichroism spectra, and fluorescence techniques in this study. Upon binding to DNA, the bis-Ru(II) complex with the longest linker (1,3-bis-(4-pyridyl)-propane), exhibited a negative LD

Comparison of the Binding Modes of (Ru(2,2'-bipyridine)3) 2+ and (Ru(2,2':6',2''-terpyridine)2) 2+ to Native DNA

Abstract: 1H-NMR and elemental analysis. Its binding mode toward DNA was compared with the well-known [Ru(bpy)3]Cl2 (bpy:2,2bipyridyl), using isotropic absorption, linear dichroism(LD) spectroscopy, and an energy minimization study. Compared to [Ru (bpy)3] 2+ , the [Ru(tpy)2] 2+ complex exhibited very little change in its absorption pattern, especially in the MLCT band, upon binding to DNA. Furthermore, upon DNA binding, both Ru(II) complexes induced a decrease in the LD magnitude in the DNA absorption region. The [Ru(tpy)2] 2+ complex produced a strong positive LD signal in the ligand absorption region, which is in contrast with the [Ru(bpy)3] 2+ complex. Observed spectral properties led to the conclusion that the interaction between the ligands and DNA bases is negligible for the [Ru(tpy)2] 2+ complex, although it formed an adduct with DNA. This conclusion implies that both complexes bind to the surface of DNA, most likely to negatively charged phosphate groups via a simple electrostatic interaction, thereby orienting to exhibit the LD signal. The energy minimization calculation also supported this conclusion.