Hyun Mee Lee

In vivo 1H-MRS evaluation of malignant and benign breast diseases.

This study was purposed to evaluate malignant and benign breast diseases on the basis of detecting choline compounds by in vivo localized 1H-MR spectroscopy. Thirty-five patients, prior to surgical treatments, including 19 cancers and 16 benign diseases were examined with breast imaging coil and inversion recovery 1H-PRESS (TR/TE/TI: 2000 ms/288 ms/160 ms) MR spectroscopy. Detection of choline was compared with the results of biopsy in each case. Choline was observed in all 19 cancer patients, while it was not detected in all other benign diseases. Detecting sensitivity of choline widely varied over the cancer cases in the range of 2.4-12.7 (average SNR value of 5.4) depending on the water/fat suppression and voxel size. Localized 1H-MRS using breast imaging coil can provide excellent sensitivity and spectral resolution to detect choline compounds present in reasonably small voxel (<1.5 cm3) of breast cancer lesion. Substantially this finding would be useful for differential diagnosis between malignant and benign breast diseases on the basis of choline observation by 1H-MRS when combined use with MR imaging.

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 energetically possible. The resulting detailed structures of the three conceivable BPQ-oligonucleotide adducts are elucidated in this work.

Molecular modeling study of the norfloxacin-DNA complex.

Abstract Molecular modeling and molecular dynamics were performed to investigate the interaction of norfloxacin with the DNA oligonucleotide 5′-d(ATACGTAT)2. Eight quinolone-DNA binding structures were built by molecular modeling on the basis of experimental results. A 100ps molecular dynamics calculation was carried out on two groove binding models and six partially intercalating models. The resulting average structures were compared with each other and to free DNA structure as a reference. The favorable binding mode of norfloxacin to a DNA substrate was pursued by structural assess including steric hindrance, presence of hydrogen-bonding, non-bonding energies of the complex and presence of abnormal structural distortion. Although two of the intercalative models showed the highest binding energy and the lowest non-bonding interaction energy, they presented structural features which contrast with experimental results. On the other hand, one groove binding model demonstrated the most acceptable structure when the experimental observation was accounted. In this model, hydrogen bonding of the carbonyl and carboxyl group of the norfloxacin rings with the DNA bases was present, and norfloxacin binds to the amine group of the guanine base which protrudes toward the minor groove of B-DNA.

Molecular modeling study on the enantioselective binding of S- and R-ofloxacin to various DNA sequences.

Abstract The complex formation of S- and R-ofloxacin with the self-complementary oligonucleotides, namely d[ATAGCGCTAT]2, d[GCGATATCGC]2 and d[ATAICICTAT]2, were investigated by the molecular dynamics (MD) simulation. Four starting positions, including two intercalation positions with different insertion directions and two minor groove binding positions, were considered. The total energy of both S- and R-ofloxacin-d[ATAGCGCTAT]2 complex, in which ofloxacin binds in the minor groove of the oligonucleotide, were lower than any intercalation binding mode. For both enantiomers, formation of the complex with GC oligonucleotide is more favorable than AT and IC oligonucleotides. When S- and R-ofloxacin are compared, the S-enantiomer exhibits more favorable total energy and torsion angles in the complex formation. This result is in agreement with the experimental observation [Hwangbo et al., Eur J Pharm Sci 18, 197 (2003)]. In the complex, both enantiomers form two hydrogen bonds: one between the carbonyl group of ofloxacin and the amine group of G16 and the other between the fluorine group and the G6 amine for S-ofloxacin. However, only one hydrogen bond is formed between endocyclic hydrogen atom at the C2 position of adenine and inosine base and carbonyl group of ofloxacin, which may be the reason for the GC preferentiality of ofloxacin.

1H-NMR studies of duplex DNA decamer containing a uracil cyclobutane dimer: Implications regarding the high uv mutagenecity of CC photolesions

To determine the origin of the UV‐specific CC to TT tandem mutation at the CC site, we made a duplex DNA decamer containing a uracil cis–syn cyclobutane dimer (CBD) as the deaminated model of a cytosine dimer. Two‐dimensional 1H‐NMR spectroscopy studies were performed on this sequence where two adenines (Ade) were opposite to the uracil dimer. Two imino protons of the uracil dimer were found to retain Watson–Crick hydrogen bonding with the opposite Ade, although the 5′‐U(NH) of the dimer site showed unusual upfield shift like that of the 5′‐T(NH) of the TT dimer, which seemed to be associated with deshielding by the flanking base rather than with reduced hydrogen bonding. (McAteer et al. 1998, J. Mol. Biol. 282:1013–1032). Hydrogen bondings at the dimer site were also supported by detecting typical strong nuclear Overhauser effects (NOE) between two imino protons and the opposite Ade H2 or NH2. But sequential NOE interactions of base protons with sugar protons were absent at the two flanking nucleotides of the 5′ side of the uracil dimer and at the intradimer site, contrasting with its thymine analog where sequential NOE was absent only at the A4–T5 step. In addition, NOE cross peak for U5(NH) ↔ A4(H2) was detected, although the NOE interactions of U6(NH) with A7(H2) and A17(H2) were not observed in contrast to the thymine dimer duplex. This different local structural alteration may be affected by the induced right‐hand twisted puckering mode of cis–syn cyclobutane ring of the uracil dimer in the B‐DNA duplex, even though the isolated uracil dimer had left‐hand twisted puckering rigidly. In parallel, these observations may be correlated with observed differences in mutagenic properties between cis–syn UU dimer and cis–syn TT dimer.