• Title, Summary, Keyword: Thymine

Search Result 82, Processing Time 0.035 seconds

DFT Study of Water-Assisted Intramolecular Proton Transfer in the Tautomers of Thymine Radical Cation

  • Kim, Nam-Joon
    • Bulletin of the Korean Chemical Society
    • /
    • v.27 no.7
    • /
    • pp.1009-1014
    • /
    • 2006
  • Density functional theory calculations are applied to investigate the intramolecular proton transfer in the tautomers of thymine radical cation and its hydrated complexes with one water molecule. The optimized structures and energies for 6 tautomers and 6 transition states of thymine radical cation are calculated at the B3LYP/6-311++G(d,p) level. It is predicted that the order of relative stability for the keto and enol tautomers of thymine radical cation is the same with that of the neutral thymine tautomers, though the enol tautomers are more stabilized with respect to the di-keto form in the radical cation than in the neutral state. A new channel of proton transfer from >C5-$CH_{3}$ of thymine is found to open and have the lowest energy barrier of other proton transfer processes in thymine radical cation. The roles of hydration are also investigated with thymine-water 1 : 1 complex ions. The presence of water significantly lowers the barrier of the proton transfer, which clearly shows the assisting role of hydration even with one water molecule

Dissociation of Thymine by Low-Energy Electrons

  • Cho, Hyuck;Noh, Hyung-Ah
    • Journal of Radiation Protection and Research
    • /
    • v.45 no.1
    • /
    • pp.11-15
    • /
    • 2020
  • Background: There have been various studies to investigate the mechanisms of DNA damage from low-energy electrons. To understand the mechanism of these strand breaks, it is necessary to investigate the dissociation mechanism of the DNA constituents, that is, bases, sugars, and phosphates. Materials and Methods: We studied the dissociation of thymine base upon interaction with low-energy electrons. For this experiment, thymine powder was pressed onto the indium base and irradiated by 5 eV electrons. Results and Discussion: Non-irradiated and irradiated thymine samples were compared and analyzed using the X-ray photoelectron spectroscopic technique to analyze the dissociation patterns of the molecular bonds after low-energy electron irradiation of thymine. Conclusion: With 5 eV electron irradiation, C-C and N-C = O bonds are the primary dissociations that occur in thymine molecules.

Study on the Structure of DNA Containing a Thymine Dimer and $T_4$ Endonuclense V * DNA Complex (Thymine Dimer를 포함한 DNA와 $T_4$ Endonuclease V * DNA 복합체의 구조에 관한 연구)

  • 이봉진;유준석;임형미
    • Biomolecules & Therapeutics
    • /
    • v.2 no.1
    • /
    • pp.28-33
    • /
    • 1994
  • In order to obtain insight into the repair mechanism of DNA containing thymine photo-dimer, the conformation of the duplex d(GCGGTTGGCG).d(CGCCAACCGC) with a thymine dimer incorporated has been studied by proton NMR. NOE data show that, although the local environment around the thymine dimer is altered, the gross structural changes are relatively small. T$_4$endonuclease V exhibited a conformational change on complex formation with DNA. This conformational change occurred around histidine 16 which was close to tyrosine 129 located in the aromatic segment (WYKYY) near the C-terminus. It is likely that the interaction between T$_4$endonuclease V and DNA is strong since the complex was not dissociated up to 1.6 M NaCl.

  • PDF

Theoretical Studies on the Photochemical Reaction of Psoralens (Ⅱ) Structure-Activity Studies on the Psoralen Photoadducts (소랄렌의 광화학 반응에 대한 이론적 연구 (Ⅱ) 소랄렌 광생성물의 구조에 대하여)

  • Kim, Ja Hong;Son, Seong Ho;Yang, Gi Su;Hong, Seong Wan
    • Journal of the Korean Chemical Society
    • /
    • v.38 no.1
    • /
    • pp.8-12
    • /
    • 1994
  • The structure-activity studies are described for the photoreaction of naturally occuring psoralen with thymine. Thymine <> psoralen <> thymine photodiadducts from DNA is studied as a model for the charge transfer interaction by the semiempirical methods (PM3-CI-UHF, etc.). The relative structural activities of psoralen, and photoadducts are analyzed in terms of their differing abilities of psoralen and photoadducts are investigated both with regard to their abilities to complex and to intercalate with thymine base. The photoadducts were inferred to be a trans-anti Psoralen(3,4) <> Thymine(5,6) and cis-anti Thymine(5,6) <> (4',5')Psoralen(3,4) <> Thymine.

  • PDF

Theoretical Studies on the Photochemical Reaction of Psoralen Derivatives with Thymine(Ⅳ). Photoadducts of Azapsoralen with Thymine (소랄렌 유도체와 티민의 광화학 반응에 관한 이론적 연구(Ⅳ). 아자소랄렌과 티민의 광생성물의 구조)

  • Kim, Ja Hong;Sohn, Sung Ho;Yang, Kee Soo;Hong, Sung Wan
    • Journal of the Korean Chemical Society
    • /
    • v.39 no.5
    • /
    • pp.338-343
    • /
    • 1995
  • The electronic structure of photoskinsensitizing 8-azapsoralen and 4,4',5'-trimethyl-8-azapsoralen has been investigated by the semiempirical (PM3-CI-UHF, etc) methods. The formation of molecular complexes between ground thymine and excited azapsoralen is discussed in terms of charge transfer interaction. The results indicated that the most probable orientation through C4-cycloaddition of 3,4-double bond of azapsoralen and 5,6-double bond of thymine bases, expecially photoadducts were inferred to be a trans-anti azapsoralen(3,4) < > Thymine(5,6) and trans-anti 4,4',5'-trimethyl-8-azapsoralen (3,4) < > Thymine(5,6).

  • PDF

The Effect of Antibiotics on the DNA Synthesis and Base Composition in Fungal Cells (진균류의 DNA 생합성 및 염기조성에 미치는 항생물질의 효과)

  • Park, Kyou-Yeon;Lee, Chong-Sam
    • The Korean Journal of Mycology
    • /
    • v.22 no.4
    • /
    • pp.366-377
    • /
    • 1994
  • The base composition of DNA of Aspergillus phoenicis, Rhizopus acidus and Candida albicans treated with cycloheximide and nalidixic acid during the culture was analyzed to compare with the control. The contents of base in the DNA were inhibited by cycloheximide, 20.4% of adenine, 43.1% of thymine, 40.9% of cytosine, 35.3% of guanine, 32.2% of purine, and 42.7% of pyrimidine for A. phoenicis. In R. acidus, 34.2% of adenine, 42.1% of thymine, 38.0% of cytosine, 18.1% of guanine, 24.1% of purine and 40.0% of pyrimidine were depressed by cycloheximide. In the antibiotic treatment of C. albicans, 58.3% of adenine, 58.5% of thymine, 58.1% of cytosine, 42.4% of guanine, 46.8% of purine and 58.8% of pyrimidine were inhibited to compare with the control. The nalidixic acid treatments were showed that, in A. phoenicis 41.6% of adenine, 47.1% of thymine, 59.3% of cytosine, 46.3% of guanine, 45.6% of purine and 57.2% of pyrimidine were inhibited. When R. acidus was treated with nalidixic acid, 59.1% of adenine, 54.7% of thymine, 35.3% of cytosine, 37.4% of guanine, 45.9% of purine and 44.9% of pyrimidine decreased. In treatment of nalidixic acid, the content of DNA was depressed 60.1% of adenine, 68.6% of thymine, 60.7% of cytosine, 40.0% of guanine, 45.8% of purine and 63.5% of pyrimidine for C. albicans In the DNA synthesis of three fungal cells, cycloheximide and nalidixic acid treatments were analyzed obviously that the biosynthesis of pyrimidine was depressed than that of purine. Therefore, it was showed that the DNA contents in the various fungal cells were inhibited remarkably in nalidixic acid treatment than cycloheximide.

  • PDF

Photoreaction of 8-Methoxypsoralen with Thymine

  • Shim, Sang-Chul;Kim, Yong-Zu
    • Bulletin of the Korean Chemical Society
    • /
    • v.4 no.2
    • /
    • pp.95-99
    • /
    • 1983
  • Photoreaction of 8-methoxypsoralen (8-MOP) with thymine (${\ge}$ 300 nm) was carried out in the dioxane-water frozen state. One major and two minor monoaddition products between 8-MOP and thymine were isolated by various chromatographic methods. Major monoadduct was characterized to be a C4 cycloaddition product formed between 5,6-double bond of thymine and 3,4-double bond of 8-MOP with cis-anti stereochemistry. Two minor adducts were proved to be stereoisomers of this major adduct.

  • PDF

Development of in vitro Short-term Carcinogenicity Test Method and its Mechanism of Action

  • Cho, Dae-Hyun;Kim, Jun-Gyou-;Ahn, Mi-Young;Park, Mi-Kyung-;Moon, Byung-Woo;Moon, Hwa-Hwey;Lee, Byung-Mu-
    • Proceedings of the Korean Society of Applied Pharmacology
    • /
    • /
    • pp.336-336
    • /
    • 1994
  • In order to develope the in vitro short term screen-ing method for carcinogen, we studied a purification method for thymine glycol in oxidaized DNA. Thymine glycol (5,6-dihydroxy-5, 6-dihydrothymine) is the major stable radiolysis poduct in thymine by chemical oxidants and ionzing radiation and it is a useful biomarker among oxidized DNA adducts, related with carcinogenests. Standard thymine glycol was prepared by oxidation of 〔$^3$H〕 thymine with KMnO$_4$ followed by purification with HPLC-LSC system and it was assayed by TLC and gas chromatography-MSD. 〔$^3$H〕 DMA adducts was isolated from E. coli (wild type ) treated with oxidative agents such as benzo(a)pyrene, adriamycin, aflatoxin B$_1$ and KBrO$_3$. These oxidative agents generated free radicals in cells by oxidative metabolism. As a result, thymine glycol was produced in cultured E. coli by four chemicals. This result shows that this methodology should be useful tool in screening oxidative carcinogen.

  • PDF

The Effect of Water in Four Adenine-Thymine and Three Guanine-Cytosine Pairs: Combining Quantum and Statistical Mechanics

  • Lee, Jinkeong;Ham, Sihyun
    • Proceeding of EDISON Challenge
    • /
    • /
    • pp.151-155
    • /
    • 2015
  • The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

  • PDF