核酸修饰碱基对的理论研究
摘要
核酸是生命遗传信息的载体,核酸内存在大量的碱基,各种碱基均为含有氮原子共轭体系的杂环化合物,在其所处的环境中弱相互作用广泛存在,其中碱基间的氢键作用对核酸的结构与复制有重要作用。本文采用量子化学二阶微扰理论(MP2)方法对核酸中的碱基间氢键作用进行理论研究,考察碱基的各种氧化损伤对Watson crick碱基对G:C和A:T的影响,以及各种氧化损伤碱基的配对性质,围绕分子间相互作用的理论方法,对碱基单体间氢键相互作用的特征及本质进行了系统的分析。主要内容如下:
1.采用MP2/6-31G**方法,对核酸碱基A, C, G, T以及19种常见的氧化损伤碱基进行结构优化,经过频率分析验证为能量低点,得到稳定构型,然后对碱基单体进行几何参数的比较,并且进行自然键轨道理论(NBO)分析,得到不同位置的氧化损伤对碱基结构以及性质的影响。结果表明,氧化损伤碱基fapy-A, fapy-G, 5-OH-6H-T, 6-OH-5H-T, T-glycol, C-glycol, U-glycol, Iso-acid呈现非平面结构,并且采用‘原子偏离碱基平面最大距离’的方法来表示碱基的非平面性。
2.采用MP2/6-31G**和MP2/6-311++G**方法,研究了19种DNA损伤碱基分别与四种正常碱基(A, C, G, T)间可能形成的碱基对,分析碱基不同位置的氧化损伤对G:C, A:T碱基对构型与强度的影响,并且考察损伤碱基的配对性质,比较各自与四种碱基间的配对强度。对于碱基对中的氢键作用,采用自然键轨道理论方法(NBO)和分子中原子理论(AIM)进行分析。通过研究表明,2-OH-A:T相对于碱基对A:T的结合能增加25%,而5-OH-U:G, 5,6-OH-U:G, Iso-acid:G, U-glycol:G和xanthosine:C相对于碱基对G:C的结合能分别降低39%,40%,44%,42%和53%,其余影响在6%内。结果表明,修饰碱基5-OH-C,5-OH-U, U-glycol,8-oxo-G , xanthosine, 8-oxo-A, fapy-A容易发生碱基错配,分别容易导致CG→GC,CG→TA, CG→TA, GC→TA, GC→CG, AT→CG,AT→GC形式的突变。
3.采用超分子方法,研究了RNA中嘧啶稀有碱基DHU和s4U分别与四种RNA碱基A, C, G, U间形成的不同碱基对,能量分析表明,它们与碱基鸟嘌呤G形成的碱基对结合能最大。
4.为了分析结合能与几何参数之间的关系,计算了结合能与碱基对中碱基平面角度间的关系,以及结合能与碱基对氢键中供体-受体间距离的关系,列出了结合能与几何参数间的关系曲线。并且考察了氢键临界点的电子密度与氢键键长间的关系,以及二阶稳定化能与氢键键长间的关系,并且针对不同质子受体的氢键建立了电子密度与键长间的趋势方程。
本论文采用的二阶微扰理论MP2方法适用于所研究体系,计算满足精度与效率要求,同时总结出将‘结合能变化率’、‘距离变化率’、‘二面角变化率’三个参数用于评估碱基对的稳定性,研究结果与实验报道结果相似,此研究可为核酸结构研究与基因突变研究提供资料。
There are enormous bases in the nucleic acid, which is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. Nucleobases are heterocyclic aromatic organic compounds containing nitrogen atoms. There are various interactions between the bases, and the hydrogen bonding interaction is very important to the structure and property of nucleic acid. In this study, the hydrogen bonding interaction between the nucleic acid bases were investigated by quantum chemistry MP2 method. The effect of oxidation on the stability of G:C and A:T base pairs and the pairing properties of the damaged bases were studied by supermolecular method.
The character and essence of the hydrogen bonds between the bases were analyzed systematicly. The main results are as follows:
1. The DNA bases A, C, G, T and 19 oxidized bases were optimized at MP2/6-31G** level and characterized as minimum by frequency analysis. Subsequently the Natural Bond Orbital (NBO) analysis was performed starting from the optimized geometries. The difference between the normal bases (A, C, G, T) and the oxidized bases were analyzed by the geometry parameters, the atom charge and bond orbitals. The results indicate that some of the damaged bases, such as fapy-A, fapy-G, 5-OH-6H-T, 6-OH-5H-T, T-glycol, C-glycol, U-glycol and Iso-acid, show the nonplanar structures, and the‘maximum distance of the atom deviate from the base plane’was used to indicate the noplanarity of the damaged bases.
2. The hydrogen bonds between 19 oxidized bases and four normal bases (A, C, G, T) were studied by supermolecule method at MP2/6-31G** and MP2/6-311++G** levels, the effect of oxidation on the configuration and strength of Watson crick base pairs G:C and A:T were discussed. The pairing properties of the damaged bases were studied by comparing the hydrogen bonding strength between the damaged bases and the normal bases. The Natural Bond Orbital (NBO) and Atoms in molecules theory (AIM) analysis were performed to compare the pairing ability to nucleic acid bases. The results indicate that base pair 2-OH-A:T increase the binding energy of A:T by 25%, while the base pairs 5-OH-U:G, 5,6-OH-U:G, Iso-acid:G, U-glycol:G and xanthosine:C decrease the binding energy of G:C by 39%,40%,44%,42% and 53%, and the ratio of binding energy change of the rest pairs are within 6%. Moreover, the results show that the favorable mispairing bases are 5-OH-C,5-OH-U, U-glycol,8-oxo-G, xanthosine, 8-oxo-A, fapy-A, and subsequently cause to the gene mutation of CG→GC,CG→TA, CG→TA, GC→TA, GC→CG, AT→CG,AT→GC.
3. The hydrogen bonds between the damaged U bases (DHU and s4U) and RNA bases (A, C, G, U) were studied by supermolecule method. The binding energies, NBO analysis and AIM analysis were performed, and the results show that they form the most binding energy pairs with base G.
4. To investigate the relationship between the interaction energy and geometry parameters, we have calculated the dependence of interaction energy on the buckle angle and the distance between the hydrogen bond donor and acceptor between bases. Furthermore, the relation between the electron density and distance, and the relation between the E(2) and distance were discussed in detail.
The MP2 method of M?ller–Plesset perturbation theory is suitable in the studied systems, which gives an approving calculation accuracy and efficiency. Moreover, the three parameters‘ratio of binding energy change’,‘ratio of distance change’,‘ratio of dihedral angle change’, were proposed to compare the stability of damaged base pairs in nucleic acid, the results are similar to the reported experimental results and these can be useful for the nucleic acid study and gene mutation research.
1.采用MP2/6-31G**方法,对核酸碱基A, C, G, T以及19种常见的氧化损伤碱基进行结构优化,经过频率分析验证为能量低点,得到稳定构型,然后对碱基单体进行几何参数的比较,并且进行自然键轨道理论(NBO)分析,得到不同位置的氧化损伤对碱基结构以及性质的影响。结果表明,氧化损伤碱基fapy-A, fapy-G, 5-OH-6H-T, 6-OH-5H-T, T-glycol, C-glycol, U-glycol, Iso-acid呈现非平面结构,并且采用‘原子偏离碱基平面最大距离’的方法来表示碱基的非平面性。
2.采用MP2/6-31G**和MP2/6-311++G**方法,研究了19种DNA损伤碱基分别与四种正常碱基(A, C, G, T)间可能形成的碱基对,分析碱基不同位置的氧化损伤对G:C, A:T碱基对构型与强度的影响,并且考察损伤碱基的配对性质,比较各自与四种碱基间的配对强度。对于碱基对中的氢键作用,采用自然键轨道理论方法(NBO)和分子中原子理论(AIM)进行分析。通过研究表明,2-OH-A:T相对于碱基对A:T的结合能增加25%,而5-OH-U:G, 5,6-OH-U:G, Iso-acid:G, U-glycol:G和xanthosine:C相对于碱基对G:C的结合能分别降低39%,40%,44%,42%和53%,其余影响在6%内。结果表明,修饰碱基5-OH-C,5-OH-U, U-glycol,8-oxo-G , xanthosine, 8-oxo-A, fapy-A容易发生碱基错配,分别容易导致CG→GC,CG→TA, CG→TA, GC→TA, GC→CG, AT→CG,AT→GC形式的突变。
3.采用超分子方法,研究了RNA中嘧啶稀有碱基DHU和s4U分别与四种RNA碱基A, C, G, U间形成的不同碱基对,能量分析表明,它们与碱基鸟嘌呤G形成的碱基对结合能最大。
4.为了分析结合能与几何参数之间的关系,计算了结合能与碱基对中碱基平面角度间的关系,以及结合能与碱基对氢键中供体-受体间距离的关系,列出了结合能与几何参数间的关系曲线。并且考察了氢键临界点的电子密度与氢键键长间的关系,以及二阶稳定化能与氢键键长间的关系,并且针对不同质子受体的氢键建立了电子密度与键长间的趋势方程。
本论文采用的二阶微扰理论MP2方法适用于所研究体系,计算满足精度与效率要求,同时总结出将‘结合能变化率’、‘距离变化率’、‘二面角变化率’三个参数用于评估碱基对的稳定性,研究结果与实验报道结果相似,此研究可为核酸结构研究与基因突变研究提供资料。
There are enormous bases in the nucleic acid, which is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. Nucleobases are heterocyclic aromatic organic compounds containing nitrogen atoms. There are various interactions between the bases, and the hydrogen bonding interaction is very important to the structure and property of nucleic acid. In this study, the hydrogen bonding interaction between the nucleic acid bases were investigated by quantum chemistry MP2 method. The effect of oxidation on the stability of G:C and A:T base pairs and the pairing properties of the damaged bases were studied by supermolecular method.
The character and essence of the hydrogen bonds between the bases were analyzed systematicly. The main results are as follows:
1. The DNA bases A, C, G, T and 19 oxidized bases were optimized at MP2/6-31G** level and characterized as minimum by frequency analysis. Subsequently the Natural Bond Orbital (NBO) analysis was performed starting from the optimized geometries. The difference between the normal bases (A, C, G, T) and the oxidized bases were analyzed by the geometry parameters, the atom charge and bond orbitals. The results indicate that some of the damaged bases, such as fapy-A, fapy-G, 5-OH-6H-T, 6-OH-5H-T, T-glycol, C-glycol, U-glycol and Iso-acid, show the nonplanar structures, and the‘maximum distance of the atom deviate from the base plane’was used to indicate the noplanarity of the damaged bases.
2. The hydrogen bonds between 19 oxidized bases and four normal bases (A, C, G, T) were studied by supermolecule method at MP2/6-31G** and MP2/6-311++G** levels, the effect of oxidation on the configuration and strength of Watson crick base pairs G:C and A:T were discussed. The pairing properties of the damaged bases were studied by comparing the hydrogen bonding strength between the damaged bases and the normal bases. The Natural Bond Orbital (NBO) and Atoms in molecules theory (AIM) analysis were performed to compare the pairing ability to nucleic acid bases. The results indicate that base pair 2-OH-A:T increase the binding energy of A:T by 25%, while the base pairs 5-OH-U:G, 5,6-OH-U:G, Iso-acid:G, U-glycol:G and xanthosine:C decrease the binding energy of G:C by 39%,40%,44%,42% and 53%, and the ratio of binding energy change of the rest pairs are within 6%. Moreover, the results show that the favorable mispairing bases are 5-OH-C,5-OH-U, U-glycol,8-oxo-G, xanthosine, 8-oxo-A, fapy-A, and subsequently cause to the gene mutation of CG→GC,CG→TA, CG→TA, GC→TA, GC→CG, AT→CG,AT→GC.
3. The hydrogen bonds between the damaged U bases (DHU and s4U) and RNA bases (A, C, G, U) were studied by supermolecule method. The binding energies, NBO analysis and AIM analysis were performed, and the results show that they form the most binding energy pairs with base G.
4. To investigate the relationship between the interaction energy and geometry parameters, we have calculated the dependence of interaction energy on the buckle angle and the distance between the hydrogen bond donor and acceptor between bases. Furthermore, the relation between the electron density and distance, and the relation between the E(2) and distance were discussed in detail.
The MP2 method of M?ller–Plesset perturbation theory is suitable in the studied systems, which gives an approving calculation accuracy and efficiency. Moreover, the three parameters‘ratio of binding energy change’,‘ratio of distance change’,‘ratio of dihedral angle change’, were proposed to compare the stability of damaged base pairs in nucleic acid, the results are similar to the reported experimental results and these can be useful for the nucleic acid study and gene mutation research.
引文
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