• Bulletin of the Korean Chemical Society
• /
• v.35 no.12
• /
• pp.3532-3534
• /
• 2014

In theoretical simulations of proton transfer in DNA, environmental factors nearly have not been considered. In our calculations, using QM/MM method on the basis of CP2K, proton transfer on adenine-thymine base pair is studied in water, at wide scope temperature, and under the external electric field. Our results indicate that the external electric field induces the proton transfer at room temperature, and its intensity and temperature have some effect on hole localization and proton transfer.

• Proceedings of the Korean Society of Potoscience Conference
• /
• 2006.06a
• /
• pp.44-44
• /
• 2006

• Bulletin of the Korean Chemical Society
• /
• v.14 no.4
• /
• pp.487-490
• /
• 1993

A semiempirical methods (PM3-CI-UHF. etc.) for the evaluation of ground and excited state electronic structures of psoralens are applied to angelicin with thymine. The photocycloaddition reaction of angelicin with thymine were deduced to be formed by their preferable HSOMO-LUMO interactions. The photoadduct was inferred to be a C$_{4-}$cycloaddition product with the stereochemistry of cis-anti formed through [2+2] addition reaction between, the 3,4 double bonds of angelicin and the 5,6-double bond of thymine.

• Proceedings of the Korean Society of Applied Pharmacology
• /
• 1994.04a
• /
• pp.267-267
• /
• 1994

In order to obtain insight into the mechanism by which DNA containing a thymine photo-dimer is recognized by the excision repair enzyme, T$_4$ endonuclease V, we have taken NMR study of this protein and its complex with oligonucleotides. The conformations of five different DNA duplexes DNA I : d(GCGGATGGCG).d(CGCCTACCGC), DNA II d(GCGGTTGGCG) .d(CGCCAACCGC), DNA III : d(GCGGT ^ TGGCG) .d(CGCCAACCGC), DNA IV d(GCGGGCGGCG).d(CGCCCGCCGC) and DNA V d(GCGGCCGGCG) . d(CGCCGGCCGC) were studied by $^1$H NMR. The NMR spectra of these five DNA duplexes in the absence of the enzyme clearly show that the formation of a thymine dimer within the DNA induces only a minor distortion in the structure, and that the overall structure of B type DNA is retained. The photo-dimer formation is found to cause a large change in chemical shifts at the GC7 base pair, which is located at the 3'-side of the thymine dimer, accompanied by the major conformational change at the thymine dimer site. The binding of a mutant T$_4$ endonuclease V (E23Q), which is unable to digest DNA containing a thymine dimer, to the DNA duplex d(GCGGT ^ TGGCG)ㆍd(CGCCAACCGC) causes a large down-field shift in the imino proton resonance of GC7. Therefore, this position is thought to be either the crucial point of the interaction wi th T$_4$ endonuclease V, or the si to of a conformational change in the DNA caused by the binding of T$_4$ endonuclease V. Usually, it is very difficult to assign NMR peaks in DNA * protein complex because of severe peak overlaps. In order to overcome these peak overlaps, we used a method of deuterium incorporation.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
• /
• 2014.10a
• /
• pp.358-360
• /
• 2014

For the several decades, various nanomaterials are broadly used in industry and research. With the growth of nanotechnology, the study of nanotoxicity is being accelerated. Particularly, mercury ion is widely used in real life. Because the mercury is representative high toxic material, it is highly recommended to detect the mercury ion. In previous reported work, thymine-thymine mismatches (T-T) capture mercury ion and create very stable base pair ($T-Hg^{2+}-T$). Here, we performed the high sensitive sensing method for direct label free detection of mercury ions and DNA binding using Kelvin Probe Force Microscope (KPFM). In this method, 30 base pairs of thymine (T-30) is used for mercury specific DNA binding ($T-Hg^{2+}-T$). KPFM is able to detect the mercury ion because there is difference between bare T-30 DNA and mercury mediated DNA ($T-Hg^{2+}-T$).

• Journal of Photoscience
• /
• v.12 no.3
• /
• pp.185-186
• /
• 2005

The electronic structure of photoskinsensitizing psoralens has been investigated by the ab initio calculations. The photocycloaddition reaction of 8-methoxypsoralen with thymine is studied as a model for the photosensitizing reaction of psoralen with DNA bases. The photocycloadduct was inferred to be a C4-cycloaddition product with the stereochemistry of Syn, H-H, Syn, H-T formed through [2+2] addition reaction between the 3,4-double bonds of 8-methoxypsoralen and 5,6-double bond of thymine base.

• Journal of Microbiology and Biotechnology
• /
• v.8 no.3
• /
• pp.229-236
• /
• 1998

6-Substituted derivatives of 1-［(2-hydroxyethoxy)methyl］-6-(phenylthio)thymine (HEPT) were synthesized by introducing alkyl groups with the aid of chlorotrimethylsilane, and then purified ranging 40 to 81 % of yield. Because of their peculiar structures, we presumed that HEPT derivatives would contain extra biological activities other than their already known anti-human immunodeficiency viral (HIV -1) activities. In this study, we investigated the possible effects of the HEPT derivatives on bacterial growth and found their selective antibiotic activities against gram-positive strains. We could not observe the corresponding activity from a disc-zone test, but confirmed the activity by liquid cultivation. Since the growth rate of cells was easily recovered, the antibiotic function was suggested to be bacteriostatic. We also suggested that the intracellular fate of HEPT derivatives would be fast. A HEPT derivative f-3 was shown to synergize unidirectionally toward chloramphenicol (Chr). With 0.1 mM f-3, the Chr-directed growth-inhibitory curve appeared 4 hours earlier than found without the additive. Interestingly, from the data of SDS-polyacrylamide gel electrophoresis (PAGE), we found that a membrane-bound protein having a molecular weight of 70-kDa was overexpressed by f-3 in S. aureus.

• Journal of the Korean Chemical Society
• /
• v.38 no.6
• /
• pp.405-410
• /
• 1994

Molecular orbital calculations suggest that an interaction between the psoralen derivatives of excite state and the thymine of ground state is dicussed in terms of their differing abilities to molecular complex. PM3-CI-UHF indicates that photocycloadducts across the C3-C4 and C4'-C5' double bonds of the methylpsoralen and hydroxypsoralen with thymine C5-C6 double bonds were deduced to be formed by their preferable frontier orbital interactions. The electronic properties of psoralen derivatives in the ground and excited states correlate with this difference in structure-activity relationship.

• Rapid Communication in Photoscience
• /
• v.3 no.4
• /
• pp.79-80
• /
• 2014

We characterized the one-electron reduction of oligodeoxynucleotides with a 2-oxopropyl group on a thymine base ($d^{oxo}T$) and applied the reaction to the radiolytic activation of DNAzyme function. We designed a system in which the DNAzyme function of cleaving mRNA was suppressed by introduction of $d^{oxo}T$ into the strand of DNAzyme. Hypoxic X-irradiation led to recovery of the cleavage ability because the 2-oxopropyl group was removed to form unmodified DNAzyme. We characterized the DNAzyme function by monitoring the fluorescence change of fluorophore- and quencher-labeled target strands. We confirmed that the DNAzyme function could be regulated by hypoxic X-irradiation and the reaction of $d^{oxo}T$.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2014.02a
• /
• pp.415.1-415.1
• /
• 2014

Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group[1].