Comparison of the stability of thymine tautomers and the interaction of its tautomers with Na+, K+, Mg2+ and Ca2+ in gas and solvent phases

The present study compared the interactions among Na ⁺, K ⁺, Mg²⁺ and Ca²⁺, thymine and its tautomers in the gas and solvent phase, an interaction dependent upon the electronic construction of the tautomers. Three types of cation interaction with thymine and its tautomers were observed. In the first one, the metal cations interacted with a lone pair of nitrogen or oxygen of the tautomers. In the second type, there was an interaction among the cations, nitrogen and oxygen at the same time; the last one was that of cations with the electron density of thymine π-system, where the cations were perpendicular to the ring of thymine. The interaction of metals cation with tautomers was studied in the gas and solvent phases; a comparison was then made between interactions in two phases. The interaction energy for all complexes indicated the stability of complexes, an energy which was higher in Ca²⁺ and Mg²⁺ compared with Na⁺ and K⁺. Concerning K⁺ and Na⁺, the stability of all complexes of tautomers was greater than that of thymine complexes; however, the stability of certain Ca²⁺ and Mg²⁺ complexes was lower than the complexes of thymine.     

四氯苯醌与嘧啶类核酸碱基的光化学氢抽取和电子转移反应

采用纳秒时间分辨的激光闪光光解实验技术,研究了四氯苯醌(TCBQ)分子与两种嘧啶核酸碱基(胸腺嘧啶和尿嘧啶)分子在355nm激发下的光化学反应动力学. 355 nm将TCBQ分子布居到激发三重态³TCBQ^*,高反应活性的³TCBQ^*与碱基分子发生两个平行的反应,氢抽取反应和电子转移反应,分别对应生成瞬态光谱上观测到的两个光反应产物TCBQH·和TCBQ·^-. 这两个反应同时生成的碱基自由基和碱基阳     

胸腺嘧啶低能量VUV光解离路径的实验和理论研究

利用同步辐射真空紫外光电离质谱和理论计算研究了胸腺嘧啶的光解离反应路径, 通过改变光子能量得到不同的质谱信号, 光子能量在12.0 eV时主要的碎片有m/z=98 (C₄H₆N₂₄O⁺)、97 (C₄H₅N₂O⁺)、84 (C₃H₄N₂O⁺或C<     

Self-assembly of a thymine quartet and quadruplex via an organic template

The synthesis of two hydrophobic cavitands bearing four (1) and eight (2) thymidine residues covalently linked with triazole moieties is reported. Spectral evidence indicates the adoption of a hydrogen-bonded T-quartet assembly by 1 in chloroform at low temperature and a π-stacked quadruplex by 2 in DMSO under ambient conditions.     

堆积的胸腺嘧啶体系光物理失活的动力学模拟

采用半经典动力学方法模拟了π堆积的胸腺嘧啶体系最低激发态的光物理失活过程.设置激光脉冲仅作用于一个胸腺嘧啶分子T,另一胸腺嘧啶分子T’保持基态.模拟发现由于T与T’之间存在π堆积相互作用,导致电荷转移,形成T带负电荷、T’带正电符的激基复合物.由于相邻分子的空间效应阻碍了激发的T分子到达圆锥相交所必需的强烈扭曲,激基复合物的寿命比单体增长.当分子间距离缩短至0.3 nm后,T分子C₅—C₆键扭曲程度最大,此时发生电荷重组,两个胸腺嘧啶分子均恢复电中性.电荷重组诱导T’分子发生畸变,并在C₅’—C₆’扭曲最大时避免相交,体系衰减至基态,T和T’分子均恢复平面构型.     

Effects of Bis(aromatic) Pendants on Recognition of Nucleobase Thymine by Zn2+ -1,4,7,10-tetraazacyclododecane (Zn2+ -cyclen)

We have previously shown that the nucleobase thymine binding to Zn²⁺ -cyclen (cyclen=1,4,7,10-tetraazacyclododecane) complex became stronger by appending acridine, naphthalene, or quinoline rings to the cyclen. Amongst these, the pendant bis((1-naphthyl)methyl) or bis((4-quinolyl)methyl) groups yielded the most effective thymine-recognizing Zn²⁺ -cyclen complexes [J. Am. Chem. Soc., 121 (1999) 5426]. The present study was undertaken to find causes of the bis(aromatic) ring effect by X-ray crystal structure analysis and NMR studies. The crystal structure of the Zn²⁺ -bis((1-naphthyl)methyl)-cyclen complex with a deprotonated 1-methylthymine (1-MeT) failed to show the anticipated evidence for the double ~ - ~ stacking interactions between the two naphthalenes and the Zn 2+ -bound 1-MeT m (1-MeT m =N(3')-deprotonated 1-MeT). Crystal data: formula C₃₆ H₄₇ N₇ O₇ Zn, M r =755.19, monoclinic, space group P2₁/ c (No. 14), a =15.438(2) Å, b =14.093(3) Å, c =16.726(2) Å, g =90.53(1) V =3638.7(8) Å 3 Z =4, R =0.035, R _w =0.049. However, the ¹H NMR studies of Zn²⁼ -bis((4-quinolyl)methyl)-cyclen with 1-MeT in varying H₂O/CH₃ CN solution showed increasing upfield shifts of Me(5') and H(6') of the Zn²⁺ -bound 1-MeT in more aqueous media, indicating that the double intercalation with the two quinolines became more significant in more protic environments. We conclude that the double ~ - ~ stacking effect accounts for the enhanced recognition of thymine base by the appended bis((1-naphthyl)methyl) or bis((4-quinolinyl)methyl) groups.     

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 C₄H₆N₂₄O⁺、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.     

Ab initio and DFT theory studies of interaction of thymine with formaldehyde

In this article, the interaction of formaldehyde (FA) with thymine is theoretically investigated by computational chemistry methods. The optimization geometries and vibrational frequencies of FA, thymine and three complexes between thymine and FA have been calculated by using the density functional theory and ab initio methods at the B3LYP/6-311G(d, p) and MP2/6-311G(d, p) levels. The NBO and AIM methods are used to analyse interaction as well. Conformers (A), (B) and (C) are cyclic structures with C–H***O and N–H***O hydrogen bonds on a common plane. The corrected complex interaction energies of cyclic structures (A), (B) and (C) at MP2/6-311G(d, p) levels are −38.41, −26.94 and −26.01 kJ/mol, respectively. The order of stability is (A) > (B) > (C).     

Analysis of ultrafast relaxation in photoexcited DNA base pairs of adenine and thymine

The photoinduced dynamics in base pairs of adenine and thymine were analyzed by femtosecond pump-probe spectroscopy. On the short-time scale up to a few picoseconds, the characteristic time constants for the dimers are quite similar to the corresponding values of the monomers. This leads to the conclusion that ultrafast intramolecular relaxation proceeds via ππ^* and nπ^* states of one component within the dimer. On the long-time scale, we obtained a novel time constant of roughly 40 ps for the thymine dimer and the adenine–thymine base pair. This time constant was never observed in the monomers and is tentatively assigned to an intermolecular relaxation process, possibly via a hydrogen transfer state.     

Analysis of Pseudouridine by Fluorescence Spectrometry

Abstract

Fluorescence spectral properties of pseudouridine, an important biological indicator, have been measured for the first time in this study. The fluorescence quantum yield is maximal in aqueous solution with pH values above 9 with spectral properties characteristic of 5 alkyl substituted uracil derivatives. Chromatographic analysis shows the fluorescence is associated only with the pseudouridine peak. The concentration dependence of fluorescence is linear from 4 to 45 micromolar at pH 11.5. The excitation maximum is about 295 nm and the emission is broad with a maximum at about 390 nm. Addition of pseudouridine to urine extracts gives a linear increase in fluorescence with increasing pseudouridine concentration.