M-RNA碱基复合物(M=Ca~+和Mg~+)特征振动的密度泛函理论分析

采用密度函数理论的B3LYP交换关联能泛函在6-311+G(2df,2p)基组水平上,优化计算了Ca+,Mg+与RNA碱基嘧啶各同分异构体形成稳定复合物的结构,发现其中C1M,T1M和U1M(M=Ca+和Mg+)为最稳定复合物,并对这些复合物红外振动进行了计算.计算结果显示碱基嘧啶单体主要存在的两个红外特征振动,是由环振动和环外氧原子及与其成键的环上碳原子之间产生伸缩振动引起的.当形成复合物时,由于离子的参与,使单体碱基分子的振动情况发生了改变,主要表现在离子倾向于与环外负电子原子N和O原子成键,使与离子直接作用环外原子参与的特征振动频率减小,谱线红移;不与离子直接作用环外原子引起的特征振动频率增大,谱线蓝移.     

Thermal Stability of Modified i‐Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

In continuation of our investigation of characteristics and thermodynamic properties of the i‐motif 5′‐d[(CCCTAA)₃CCCT)] upon insertion of intercalating nucleotides into the cytosine‐rich oligonucleotide, this article evaluates the stabilities of i‐motif oligonucleotides upon insertion of naphthalimide (1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) as the intercalating nucleic acid. The stabilities of i‐motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (T_m) and circular dichroism spectra at different pH values and conditions (crowding and non‐crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i‐motif structures compared to the wild‐type structure which is in contrast to a previous observation for a pyrene‐intercalating nucleotide showing a decrease in T_m values.     

On the affinity of cytosine towards electrophiles

Ab initio SCF computations on the intrinsic preferences of the H⁺, CH ₃ ⁺ and C₂H ₅ ⁺ cations towards the two principal sites of protonation or alkylation on cytosine, N₃ or O₂, show that this preference undergoes a continuous modification with the increase in size and complexity of the cation. N₃ is the preferred site of fixation of H⁺, O₂ the preferred site of C₂H ₅ ⁺ , while CH ₃ ⁺ has no marked preference. The exchange repulsion term of the binding energy appears responsible for the preference of C₂H ₅ ⁺ for O₂.This work was supported by the Ligue Francaise contre le Cancer and the National Foundation for Cancer Research (USA)     

Hydration scheme of uracil and cytosine

The comparison of a pure electrostatic approximation and complete supermolecule SCF ab initio computations on the hydration scheme of uracil and cytosine shows that the electrostatic procedure is capable to reproduce the general aspects of the results of the supermolecule treatment provided that different distances of shortest approach be adopted for the distances between the oxygen of water and the nitrogen of NH₂ or NH groups or the oxygen of C-O groups on the one hand and the oxygen of water and pyridine-type nitrogens on the other hand.     

Water effect on the excited-state decay paths of singlet excited cytosine

Two low-energy deactivation paths for singlet excited cytosine, one through a S₁/S₀ conical intersection of the ethylene type, and one through a conical intersection that involves the (n_N, π^*) state, are calculated in the presence of water. Water is included explicitly for several cytosine monohydrates, and as a bulk solvent, and the calculations are carried out at the complete active space self-consistent field (CASSCF) and complete active space second order perturbation (CASPT2) levels of theory. The effect of water on the lowest-energy path through the ethylenic conical intersection is a lowering of the energy barrier. This is explained by stabilization of the excited state, which has zwitterionic character in the vicinity of the conical intersection due to its similarity with the conical intersection of ethylene. In contrast to this, the path that involves the (n_N, π^*) state is destabilized by hydrogen bonding, although the bulk solvent effect reduces the destabilization. Overall, this path should remain energetically accessible.     

白菜DNA甲基化水平的反相离子对高效液相色谱法研究

建立了反相离子对液相色谱测定白菜的DNA甲基化水平的方法。采用的色谱柱为HypersilBDSC18柱(200mm×4.0mm,5μm),以pH4.0的甲醇-5mmol·L-1庚烷磺酸钠-三乙胺(10:90:0.2,体积比)的混合液为流动相,UV检测器波长为273nm。通过测定DNA水样所产生的胞嘧啶和甲基胞嘧啶的含量,即可得知DNA甲基化程度。胞嘧啶和甲基胞嘧啶回收率分别为99.6%及103.3%,RSD为3.7%(日内)及5.2%(日间)。     

胞嘧啶水溶液体系辐解的瞬态产物研究

Using the ns pulse radolysis, we studied the characteristic absorption spectrum and kinetic decay of cytosine anion radical (Cyt-). Results showed that the characteristic absorption of Cyt- was located at λ=355±5 nm, and decayed following the first order kinetics with τ1/2=265 ns at pH=7.0. The decay became slower and τ1/2 rapidly rised with the increment of pH value, Cyt- protonated at C6 in acidic solution, and the characteristic absorption was located at λ=310±5 nm, and decayed following the second order kinetics: Cyt- protonated at N3 in aqueous solution of pH≥7, and the characteristic absorption was located at λ=295±5 nm, and decayed following the second order kinetics.     

5-甲基胞嘧啶及胞嘧啶无辐射失活的半经典动力学模拟和CASSCF计算

采用半经典动力学方法模拟了5-甲基胞嘧啶(5m-Cyt)和胞嘧啶(Cyt)在267 nm紫外光辐射下的光物理失活过程. 模拟发现, 5m-Cyt 和Cyt 的激发态通过C₅－C₆键的扭曲以及甲基(或H₅)和H₆原子平面外振动失活.失活时, 甲基(或H₅)和H₆原子几乎与环面垂直并指向不同方向, 形成“双自由基态”. 由于甲基的体积比H原子的大, 振动频率较小, 使得C₅原子的变形受到抑制, 导致5m-Cyt 的激发态寿命比胞嘧啶更长. 完全活性空间自洽场(CASSCF)计算显示, 5m-Cyt的圆锥交叉(CI)点能量比Cyt 高0.3 eV, 这也证明5m-Cyt演化至CI 需要克服更大的能垒, 因此激发态寿命长于胞嘧啶.     

Selective Determination of Cytosine Based on Its Fluorogenic Reaction with Triethylamine/Chloroacetonitrile

Abstract

A sensitive fluorometric method is described For selective determination of cytosine in nucleobases. The method is based on chemical derivatization of cytosine by triethylamine/chloroacetonitrile. The effects of solvent, reaction temperature, reaction time and concentration of reagents on the efficiency of the reaction were studied. A good linear relationship between fluorescence intensities and cytosine concentrations in the range of 2.0–800 ng/mt was observed. The detection limit for cytosine is 0.6 ng/ml (S/N=3). The relative standard deviations (7 replicates) for measurements of 50 and 500 ng/ml cytosine were 2.1 and 2.5%, respectively.     

Potential of metal–fullerene hybrids as strong nanocarriers for cytosine and guanine nucleobases: A detailed DFT study

In this article, the adsorption of cytosine and guanine molecules on the surface of Cr-doped C20 fullerene (C19Cr) and Ni-doped C20 fullerene (C19Ni) are studied using first-principles density functional theory (DFT) calculations. In order to thoroughly comprehend the influences of the molecules on the metal-fullerene complexes, the geometric parameters, the binding energies, transferred charges, the magnitude of dipole moments, thermochemical parameters, frontier molecular orbitals, and the global indices of activities are calculated. The results highlighted that the interactions of both cytosine and guanine molecules with metal-fullerene complexes are highly exothermic, suggesting that these molecules might be chemisorbed on their adsorbents. The C19Cr exhibits a better adsorption behavior toward the molecules compared to C19Ni, and cytosine has the higher binding energies with metal-fullerene complexes in comparison with guanine. Further analyses showed that the C19Cr experiences significant changes in its electronic properties upon adsorption of the cytosine molecule. However, the small variations in the electronic properties of C19Ni after complexation with guanine indicate that this complex is not sensitive to the guanine. Furthermore, the results of frontier molecular orbital reveal the strong (moderate) interactions between the C19Cr with the cytosine (guanine) molecule and moderate (weak) interactions between the C19Ni with the cytosine (guanine) molecule. Therefore, the C19Cr and C19Ni have moderate sensitivities to cytosine and guanine molecules. More excitingly, our findings divulge promising potential of the Cr-fullerene complex as a biochemical adsorbent for cytosine.