Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines

Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites （Site 1, Site 2, and Site 3） that can induce strong directional N-H...O=C hydrogen bonding interaction. In this paper, theoretical calculations are carded out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil （or thymine） would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.

大气压低温等离子体与胸腺嘧啶脱氧核苷的作用

胸腺嘧啶(Thymine)是遗传物质的组成成分之一,为了研究等离子体对遗传胸腺嘧啶(Thymine)的作用过程,利用大气压等离子体对作为遗传物质的胸腺嘧啶(Thymine)及对应的胸腺嘧啶脱氧核苷(Thymidine)进行处理,为了避免空气对遗传物质的影响,采用水中放电装置进行了相关研究。研究结果表明:不同气体等离子体处理后,胸腺嘧啶脱氧核苷会分解为胸腺嘧啶,且氮气等离子体处理时分解速率快于氩气等离子体处理;另外,空气等离子体与氧气等离子体处理后,胸腺嘧啶脱氧核苷会分解产生两种新产物,分别为胸腺嘧啶+OH和胸腺嘧啶脱氧核苷+OH。该研究对了解大气压等离子体对细菌失活的机制具有一定指导作用,同时对等离子体与生物体作用有着积极的指导意义。

Photochemical Hydrogen Abstraction and Electron Transfer Reactions of Tetrachlorobenzoquinone with Pyrimidine Nucleobases

Pentachlorophenol, a widespread environmental pollutant that is possibly carcinogenic to humans, is metabolically oxidized to tetrachloroquinone （TCBQ） which can result in DNA damage. We have investigated the photochemical reaction dynamics of TCBQ with two pyrimidine type nucleobases （thymine and uracil） upon UVA （355 ran） excitation using the technique of nanosecond time-resolved laser flash photolysis. It has been found that 355 nm excitation populates TCBQ molecules to their triplet state 3TCBQ＊, which are highly reactive towards thymine or uracil and undergo two parallel reactions, the hydrogen abstraction and electron transfer, leading to the observed photoproducts of TCBQH. and TCBQ.- in transient absorption spectra. The concomitantly produced nucleobase radicals and radical cations are expected to induce a series of oxidative or strand cleavage damage to DNA afterwards. By characterizing the photochemical hydrogen abstraction and electron transfer reactions, our results provide potentially important molecular reaction mechanisms for understanding the carcinogenic effects of pentachlorophenol and its metabolites TCBQ.

Dissociation Pathway Analysis of Thymine under Low Energy VUV Photon Excitation

Photon-induced dissociation pathways of thymine are investigated with vacuum ultraviolet photoionization mass spectrometry and theoretical calculations. The photoionization mass spectra of thymine at different photon energy are measured and presented. By selecting suitable photon energy, exclusively molecular ion m/z=126 is obtained. At photon energy of 12.0 eV, the major ionic fragments at m/z=98, 97, 84, 83, 70, and 55 are obtained, which are assigned to C4H6N2O＋, C4H5N2O＋, C3H4N2O＋ （or C4H6NO＋）, C4H5NO＋, C2NO2＋, and C3H5N＋, respectively. With help of theoretical calculations, the detailed dissociation pathways of thymine at low energy are well established.

Theoretical Study on the Reaction of Thymine with Iodomehane in the Water Phase

The reaction mechanisms of carcinogenic methylating agent iodomethane （MeI） with keto and enol tautomers of thymine （K- and E-thymine） were studied by using the B3LYP/6-311＋G （d, p） method in water phase. The solvent effects were examined using the polarizable continuum model （PCM）. Specifically, PCM single-point calculations at the same level of theory were performed in acetone and CCl4 that represent a range in nonpolarity. The calculated results show that the reaction of K-thymine with MeI is a two-step mechanism, whereas that of E-thymine is a one-step mechanism. Our calculations reveal that K-thymine is appreciably more stable than the enol form in the water phase or in the two solvents. The K- and E-form reaction barriers are 135.6 and 222.1 kJ/mol, respectively in water phase. These findings indicate that the reactions mentioned above could not occur efficiently in biological media in the absence of catalyst. Our conclusions are in agreement with the previous studies on the reactions of guanine with methyl chloride and methyl bromide.

Synthesis of Peptoid Nucleic Acid with Thymine as Nucleic Base

The synthesis of peptoid nucleic acid bearing thymine as nucleobase has been achieved. This modified oligonucleotide showed good hybridization with DNA.

Controllable synthesis of novel mono-and di-terpyridine derivatives

A series of novel mono- and di-terpyridine derivatives with purinyl and pyrimidyl group were obtained from the reaction of 4′-p- bromomethylphenyl-2,2′：6,2″-terpyridine with 6-mercaptopurine, 2,6-dimercaptopurine and thymine, respectively. The active hydrogens on these alkaloids could be abstracted stepwise using different bases, which made the addition controllable.

Density Functional Theory Study on Interaction between Catechin and Thymine

The interacting patterns and mechanism of the catechin and thymine have been investigated with the density functional theory Becke＇s three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional （B3LYP） method by 6-31＋G＊ basis set. Thirteen stable structures for the catechin-thymine complexes have been found which form two hydrogen bonds at least. The vibrational frequencies are also studied at the same level to analyze these complexes. The results indicated that catechin interacted with thynfine by three different hydrogen bonds as N-H…O, C-H…O, O-H…O and the complexes are mainly stabilized by the hydrogen bonding interactions. Theories of atoms in molecules and natural bond orbital have been adopted to investigate the hydrogen bonds involved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error, which are from -18.15 k J/mol to -32.99 kJ/mol. The results showed that the hydrogen bonding contribute to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red-shifted relative to that of the inonomer, which is in agreement with experimental results.

Synthesis and Crystal Structure of Cis-syn Cyclobutane 1-(Carboxyethyl)thymine Dimer Monopentyl Amide Monotryptophan Methyl Ester Amide

The crystal structure of the title compound （C34H47NTO9, Mr = 697.79） has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000（8）, b = 11.360（10）, c = 17.841（15.）/k, β = 97.083（14）°, V = 1810（3）A^3, Z = 2, F（000） = 744, D,.= 1.280 g/cm^3,/t = 0.094 mm^-1, the final R = 0.0721 and wR = 0.1942 for 2479 observed reflections with I 〉 2σ（I）. The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond （N（6）-H（6）…O（8）） introduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.

Theoretical Study of Interaction between Apalutamide Anticancer Drug and Thymine by DFT Method

The main purpose of this study is a better comprehension of the non-bonded interaction between an anticancer drug apalutamide and deoxyribonucleic acid(DNA).In the prese nt work,the in teraction between an ticancer drug apalutamide and one of the DNA bases called 2,-deoxythymidine 5,-monophosphate(thymine)by Density Functional Theory(DFT)calculations in the solvent water has been investigated for the first time.The non-bonded interaction effects of the molecule apalutamide with thymine on the electronic properties,chemical shift tensors and natural charges have been also detected.The natural bond orbital(NBO)analysis was performed for determining the role of electron donor and acceptor of the molecules apalutamide and thymine at the complex thymine/apalutamide.Both Electron location function(ELF),localized orbital locator(LOL)and quantum theory of atoms in molecules(QTAIM)analysis were carried out in order to determine the chemical bond nature in the investigated compounds.The values of ELF and LOL parameters for the selected bonds are small,which confirms the non-covalent character of these bonds in nature.The electronic spectra of the apalutamide drug,thymine and complex thymine/apalutamide in solvent water were calculated by Time Dependent Density Functional Theory(TD-DFT)for the investigation of interaction effect;Non-bonded interaction between the compound apalutamide and thymine has changed the value of λmax.

A Novel Photoproduct of Thymine in Phosphate-buffered Saline under Far UV Irradiation

The photolysis of thymine in phosphate-buffered saline (PBS, pH 8.0) under the irradiation of medium pressure mercury lamp (MPML) produces a novel compound C5H7N2O6P. The composition and structure of the compound have been identified by elemental analysis, EI-MS, UV, IR, 1H, 13C, 31P-NMR.

Theoretical Investigation on the Absence of Spore Photoproduct Analogue at Cytosine-Thymine Site

As a well known DNA photolesion product, the special UV induced pyrimidine dimmer called spore photoproduct （SP）, has aroused strong research interests. The SP formation was reported solely between two adjacent thymidine residues. It remains unclear in pervious experimental observations why there is an absence of the cytosine-derived SP-like photoprod- uct formation at the cytosine containing DNA strand, although the cytosine residue holds great similarity to thymine in terms of molecular structure. From a theoretical perspec- tive, we have explored this issue in this work by means of density functional theory at the B3LYP/6-311＋＋G（d,p） //B3LYP/6-31G（d,p） level for the DNA dinucleotide fragment, cy- tosine phosphate thymine （CpT）. Key factors blocking the formation of the SP-like product between two adjacent cytosine and thymidine residues are revealed. Instead of undergoing photochemical SP reaction, a photophysical deactivation pathway back to the ground state turns out to be favorable for the CpT dinucleotide fragment.

THYMINE BONDED-STATIONARY PHASE FOR HIGH PERFORMANCE LIQUID CHROMATOGRAPHY

A new type of HPLC stationary phase containing thymine derivative was successfully prepared.It was found to give selective separation of nucleic acid bases and several purine derivatives,such as caffeine and theophylline.The retention behaviour and elution order of the solutes were interpreted in terms of molecular structure.

Effects of herpes simplex virus thymidine kinase/acyclovir system on growth of human pulmonary adenocarcinoma A549 cell line in vitro and in vivo

Objective: To observe the effect of anciclovir (ACV) treatment on tumors induced by inoculation of TK gene-transfected human pulmonary adenocarcinoma A549 cells in nude mice. Methods: A recombinant plasmid containing TK gene was constructed and transfected into A549 cells by electroporation. The sensitivity of the transgenic cells (A549-TK) to ACV was examined by MTT assay in vitro and for in vivo observation, inoculation of A549-TK and A-549 cells into nude mice was separately performed to induce tumor growth, the response of which to ACV treatment was observed, and the tumor tissues were pathologically examined. Results: A recombinant plasmid containing TK gene was successfully constructed and transfected into A549 cells. The sensitivity of A549-TK cells to ACV was 43 times higher than that of A549 cells. The tumors induced by A549-TK cells showed no significant increase in size after ACV treatment (P>0. 05) , and light microscopy revealed local tissue necrosis, karyoklasis, and nuclei disappearance. Conclusion: A549-TK cells acquires sensitivity to ACV both in vitro and in vivo, and ACV can inhibit the growth of tumors induced by A549-TK cell inoculation in nude mice.

Kinetics and mechanism of thymine degradation by TiO_2 photocatalysis

The advanced oxidation processes were examined toward the degradation of thymine （CsH6N202）, a type of nucleic acid from the pyrimidine family. As observed, the photodegradation of thymine over TiO2 photocatalyst was rapid and significant in aqueous solution under UV irradiation. Different parameters were studied, including the adsorption of thymine onto TiO2 photocatalyst, the kinetics of degradation, and the effect of pH on the photocatalytic properties of thymine degradation. Additionally, the mineralization of the products obtained upon thymine photodegradation was studied. The disappearance and mineralization rates of thymine during the photocatalytic process were also compared and discussed. The mineralization of nitrogen was also investigated, and the identification of the intermediate products was established. Finally, electronic density calculations were used to propose possible chemical pathways for the photodegradation of thymine over TiO2 photocatalyst under UV irradiation.

Polymerase-tautomeric Model for Untargeted Delayed Base Substitution Mutations Formation during Error-prone and SOS Replication of Double-stranded DNA Containing Thymine and Adenine in Some Rare Tautomeric Forms

Polymerase-tautomeric model for untargeted delayed base substitution mutations is proposed.Structural analysis of bases insertion showed that any canonical bases may be inserted opposite rare tautomeric forms of thymine T3*,adenines A2*and A4*so that between them hydrogen bonds are formed.Canonical adenine and cytosine can be incorporated opposite canonical thymine only.Canonical thymine and guanine can be incorporated opposite canonical adenine only.If in the synthesis of DNA containing rare tautomeric forms of thymine T3*,adenines A2*and A4*,involved DNA polymerases with relatively high fidelity of synthesis,mutations not appear.However,if further DNA synthesis will involve DNA polymerases having a low fidelity of synthesis,there may be base substitution mutations.It was shown that the conclusion made in the Tomasetti and Vogelstein cancer risk model that the formation of about 67%of all mutations was not caused by exposure to any mutagens is erroneous.

AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure revealed a flexible hairpin lid and a reorganized substrate recognition loop used by AlkB to accommodate cagedT.These observations demonstrate,at the molecular level,how bulky DNA adducts may be recognized and processed by AlkB.

Repair effect of thymine radical anion by echinocoside using pulse radiolysis

Repair activities of thymine radical anion by echinocoside, isolated from Pedicularis plicata. were studied using pulse radiolysis technique. The thymine radical anion was produced by the reaction of hydrated electron with thymine. Echinocoside. one of the polyphenols of phenylpropanoid glycoside, was added to the thymine aqueous solution saturated with N2. Kinetic analysis by transient absorption spectrum showed that thymine radical anion was formed at first, and then after several decades of microseconds of pulse radiolysis. the spectrum of thymine radical anion was changed to that of echinocoside radical anion. The evidence indicated that thymine radical anion was repaired through one-electron-transfer between the DNA base radical anion and echinocoside. The rate constant of electron transfer by echinocoside was 1.45× 109 dm3 · mol1 · s 1.

Transport Selectivity of a Diethylene Glycol Dimethacrylate- Based Thymine-imprinted Polymeric Membrane over a Cellulose Support for Nucleic Acid Bases

The binding mechanism between 9-vinyladenine and pyrimidine base thymine in methanol was studied with UV-visible spectrophotometric method. Based on this study, using thymine as a template molecule, 9-vinyladenine as a novel functional monomer and diethylene glycol dimethacrylate as a new cross-linker, a specific diethylene glycol dimethacrylate-based molecularly imprinted polymeric membrane was prepared over a cellulose support. Then, the resultantly polymeric membrane morphologies were visualized with scanning electron microscopy and its permselectivity was examined using thymine, uracil, cytosine, adenine and guanine as substrates. This result showed that the imprinting polymeric membrane prepared with diethylene glycol dimethacrylate exhibited higher transport capacity for the template molecule thymine and its optimal analog uracil than other nucleic acid bases. The membrane also took on higher permselectivity than the imprinted membrane made with ethylene glycol dimethacrylate as a cross-linker. When a mixture including five nucleic acid bases thymine, uracil, cytosine, adenine and guanine passed through the diethylene glycol dimethacrylate-based thymine-imprinted polymeric membrane, recognition of the membrane for the template molecule thymine and its optimal analog uracil was demonstrated. It was predicted that the molecularly imprinted membrane prepared with diethylene glycol dimethacrylate as cross-linker might be applicable to thymine assay of absolute hydrolysates of DNA or uracil assay of absolute hydrolysates of RNA in biological samples because of its high selectivity for the template molecule thymine and its optimal analog uracil.

Determination of Hg^2＋ in Tap Water Based on the Electro- chemiluminescence of Ru（phen）3^2＋ and Thymine at Bare and Graphene Oxide-Modified Glassy Carbon Electrodes

The electrochemiluminescence （ECL） of the Ru（phen）3^2＋/thymine （T） system at bare and graphene oxide （GO）-modified glassy carbon （GC） electrodes was utilized to determine Hg2＋ in tap water. The ECL intensity of Ru（phen）3^2＋ was considerably enhanced by the addition of thymine because of the occurrence of ECL tion between them. Subsequently, the ECL intensity of Ru（phen）3^2＋/T system rapidly decreased with the addition of Ru（phen）3^2＋ because of the formation ofa T-Hg^2＋-T complex. A linear response （R2=0.9914） was obtained over a Hg^2＋ concentration range of 1.0×10 9 mol/L to 1.0×10^-5 mol/L with a detection limit of 3.4×10^-10 mol/L at a bare GC electrode in 0.1 mol/L phosphate buffer （pH=8.0）. The detection limit can be further reduced to 4.2 ×10^-12 mol/L after modification of the GC electrode by GO. To verify its applicability, the proposed method was utilized to determine Hg^2＋ in tap water and simulated wastewater. The method exhibited good reproducibility and stability and thus reveals the possibility of developing a novel ECL detection method for Hg^2＋.