DNA碱基异构化及烷基化损伤的理论研究
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摘要
DNA分子结构的任何异常变化均称为DNA损伤,包括DNA双螺旋链的断裂与交联、氨基的脱落、碱基的异构化与脱落、烷基化等等。为保证机体生理活动的正常进行、生命过程的延续和遗传的稳定性,生物体内形成了一整套相当完善的修复系统,可使DNA的损伤得到最大限度的修复。生物体内未被修复的DNA损伤是极少量的,但就是这些极少量未被修复的DNA损伤却可能对机体产生非常重大的影响。未被修复的DNA损伤在DNA下一个环节的复制中,双螺旋链核苷之间的结合就会发生错误并产生数量不足的碱基对或者发生碱基错配,导致基因突变,造成遗传性疾病或物种的变异。另一方面,基因突变对生物也不是完全有害的,一些对生物有利的突变可能被生物保留下来,最终导致生物的进化。从这个意义上说,DNA损伤亦是生物进化的必要条件。DNA的人工损伤(人工诱变)是治疗癌症及遗传性疾病的重要手段;随着基因工程的发展,DNA人工诱变越来越多的被用来改良甚至创造物种。
本论文运用量子化学方法研究了嘧啶碱基和嘌呤碱基四种碱基的异构化过程和甲基化碱基对的结构和性质,从微观角度研究了异构化机理和烷基化机理。通过对这些机理的研究对DNA损伤过程有全面,深入的认识,从而可以为抑制不良损伤和利用、开发有利损伤奠定基础并提供理论指导。这在化学以及生命科学领域均具有重大理论和实际意义。
主要研究内容及结论归纳如下:
1.利用密度泛函方法,在B3LYP/6-311+G~(**)基组水平上对所有的嘧啶异构体,过渡态分别在气相和液相中进行几何结构全优化。DNA嘧啶碱基胞嘧啶和胸腺嘧啶的异构化过程可分为原子间的质子转移和N-H键围绕C=N双键旋转两类。其中在原子间质子转移过程中,形成关键部分为平面四元环的过渡态,该四元环与碱基骨架共平面。质子通过四元环发生原子间转移。当考虑溶剂化效应时,所有的平衡态在液相中的能量小于在气相中的能量。但是所有过程的活化能却都增高。说明溶剂化效应增加反应的势垒。在气相和液相中质子转移过程的活化能大于N-H旋转过程的活化能。在研究温度范围内,直接导致碱基损伤的异构化过程,即DNA嘧啶碱基正常构型的异构化过程均属于热力学上的非自发过程;由于异构化过程仅仅涉及一个质子的键合情况的变化或位置的移动,故其熵变均很小。若可以达到异构化平衡,胞嘧啶正常构型异构化平衡常数和异构化率较大;而胸腺嘧啶正常构型发生异构化的平衡常数很小,异构化率也较小。两种异构化过程的反应速率很低。当考虑溶剂化效应时,液相中的异构化的速率会降低。
2.利用密度泛函方法在B3LYP/6-311+G~(**)基组水平上对所有的嘌呤异构体,过渡态分别在气相和液相中进行几何结构全优化。嘌呤碱基的异构化过程也可以分为原子间的质子转移和N-H围绕C=N旋转两类。其异构化过程ADE1→ADE2,GUA1→GUA2,GUA3→GUA5和GUA3→GUA7属于两个N原子间质子转移过程,GUA1→GUA3属于N原子和O原子间的质子转移,所有质子转移过程的过渡态均包括一个新形成的平面四元环,该四元环与嘌呤碱基骨架共平面。在所有N-H键围绕N=C双键的旋转过程的过渡态中,平面CNH垂直于整个分子平面。质子转移过程与N-H旋转过程相比具有更高的反应能垒,更小的反应常数和平衡常数。当考虑溶剂化效应时,所有的平衡态在液相中的能量小于在气相中的能量,除了TS-G56和TS-G78在液相中活化能小于气相中的活化能外,其它过程液相中的活化能大于气相中的活化能。热力学分析表明,四个碱基的正常构型均是异构体中热力学最稳定的构型,直接导致嘌呤碱基正常构型变化的异构化过程均属于热力学上的非自发过程;在研究温度范围内,根据平衡常数得到的最大异构化率分别约为:腺嘌呤5×10~(-8);鸟嘌呤10~(-3)。可见,两个嘌呤碱基之间的平衡损伤比率有很大差别。由Guanine引起的碱基异构化多于由Adenine引起的异构化过程。
3.用密度泛函(DFT)理论方法在B3LYP/6-31+G(d,p)基组水平上对G-C及A-T碱基对甲基异构体进行结构优化和分裂能计算研究发现,从几何构型将甲基异构体分为两类:一类是甲基加成到未参与氢键的原子上,N7-meG-C,N3-meG-C,N3-meA-T和N7-meA-T依然保持碱基对的氢键形式和配对方式,在第一次复制过程中对碱基对损伤的影响较小。另一类为甲基加成到参与氢键形成的原子上。N1-meA-T,N3′-me T-A,O4′-me T-A,O2′-me T-A,N3′-meC-G和O2′-meC-G碱基对的氢键结合形式,配对方式都发生了变化。第一次复制过程中对碱基对损伤的影响较大。O6-meG-C例外,O6原子虽然参与了氢键的形成,但O6碱基对甲基化物并未改变碱基对的氢键形式和配对方式,对碱基对损伤的影响较小。
从分裂能上分析可得,除了O2′-meC-G结构外,由于甲基是供电子基,使碱基对生成异构体的分裂能增加。甲基加成到Guanine上形成异构体的稳定性大于加成到Cytosine上形成的异构体的稳定性。G-C碱基对甲基异构体中造成DNA损伤较大的异构体其稳定性较低。甲基加成到Thymine上形成异构体的稳定性大于加成到Adenine上形成的异构体的稳定性。A-T碱基对甲基异构体中造成DNA损伤较大的异构体其稳定性反而较高。从电荷分析可以得出,氢键键长和电荷的分布与碱基对的分裂能没有直接的关系。碱基氢键间存在电荷转移,甲基加成到Cytosine上时,电荷的转移小于甲基加成到鸟嘌呤上。对于A-T碱基对来说,由于加成到TO2,TO4和TN3位后THY中H3′原子都转移到ADE的N1原子上,所以生成物中的电荷的增加都在腺嘌呤ADE上。
总之,通过对DNA异构化、甲基化过程的理论研究,初步阐明了异构化过程的反应机制和甲基化碱基对对DNA的损伤。这些结果对深刻理解DNA化学损伤过程的本质,进一步探索影响DNA化学损伤的条件和控制DNA化学损伤过程具有一定的理论和实践意义。
The DNA damage means all kinds of the abnormal changes of DNA molecular structure. Including,the breakage and crosslinkage of double helical structure of DNA chain, isomerization,deamination alkylation of DNA base.Most of DNA damages can be repaired by the repair system in biology body,which is the foundation to maintain the genetic stability.The number of un-repaired DNA damages is thimbleful,but these un-repaired damages maybe produce very important influence on organism.In the replication process,DNA damage can lead to gene mutation and bring forth senescence,tumor and other diseases related to gene. Some DNA damages may be transmitted to filial generation,which is called gene mutation in genetics.Gene mutation can do organism a lot of harm,for example,it can induce cancer.On the other hand,it may endow the cell new function,and finally result in biological evolution. Moreover,the mutation induced artificially is the important approach to improve or create species,prevent or cure cancer and other diseases related to gene.Thus the research of DNA damage mechanism is a very important subject in life science.
In this dissertation,we studied the isomerization of pyrimidine and purine base and methylating of base pair with density functional theory(DFT)calculations.Our purposes are to shed light on the mechanistic details of isomerization and methylation of DNA damage.The research of occurring and developing mechanism of DNA damage is the basis of utilizing advantageous damage and inhibiting disadvantageous damages.So it is very important research topic in biology and chemistry.
The valuable results in this dissertation can be summarized as follows:
The mechanism of DNA damage caused by the isomerization of pyrimidine base has been systematically studied by performing density functional theory calculations at the B3LYP/6-311+G(d,p)level.It is shown that the isomerizations of pyrimidine base can be classified into two types.The first is the hydrogen transfer between atoms,whose transition state includes a four-member ring.The second is the bond N-H rotation about the double bond N=C,and the plane CNH is perpendicular to the molecular plane in its transition state.The hydrogen transfer has higher reaction potential barrier,larger tunnel effect,and smaller equilibrium constant and rate constant than that of the N-H rotation.When the effects of hydration are considered in the framework of the polarizable continuum model,the two types of isomerizations will all have larger reaction barrier,larger tunnel effect and smaller rate of constant.The isomerizations leading directly to DNA damage are endothermic reaction and thermodynamic nonspontaneous processes.The DNA damage rate caused by the self-isomerization of cytosine and thymine is very slow.The probability of DNA damage caused by the cytosine isomerization is larger than that by the thymine.
The mechanism of DNA damage caused by the isomerization of purine base is studied with density functional theory calculations at the B3LYP/6-311+G(d,p)level.The transition states of all the isomerizations are obtained,and the intrinsic reaction coordinate(IRC) analyses are performed to identify these transition states further.The isomerizations of purine bases can be classified into two types.The first is the hydrogen transfer between atoms,whose transition state includes a four-member ring.The second is the bond N-H rotation about the double bond N=C,and the plane CNH is perpendicular to the molecular plane in its transition state.The hydrogen transfer has higher reaction potential barrier,larger tunnel effect,and smaller equilibrium constant and rate constant than that of the N-H rotation.Effects of the hydration are considered in the framework of the polarizable continuum model(PCM)in SCRF method at the B3LYP/6-311+G(d,p)level.The isomerizations which result in the configuration changes of purine base and bring directly the DNA damage are endothermic and thermodynamic non-spontaneous process.The probability of DNA damage caused by the guanine isomerization is larger than that by adenine.
Methylation of Watson-Crick adenine-thymine(A-T)and guanine-cytosine(G-C)base pair have been investigated by density functional theory calculations at the B3LYP/6-3 l+G(d,p) level.Calculations show that the 11 methyl isomers may be divided into two groups.(1)The methyl adds to an atom that is directly related to the hydrogen bonds of the base pair.(2)The methyl atom adds to an atom that is away from the hydrogen bonds of the base pair.In the fist group,N7-meG-C,N3-meG-C,N3-meA-T and N7-meA-T maintaining the planar structure of base pair have less influence on base pair damage.In the second group,N1-meA-T,N3′-me T-A,O4′-me T-A,O2′-me T-A,N3′-meC-G and O2′-meC-G which changes base pairing sequence,may cause a major lesion of DNA.
Except O2′-meC-G,the base pairing energy of other isomers are increase because the methyl is donor group.Isomers of methylating guanine are more stable than the isomer of methylating cytosine.Isomers of methylating thymine are more stable than isomer of methylating adenine.There is no direct relationship between the charge distribution and the stabilization energy.Charge transfer exists in base pair,when the methyl adds to the cytosine, charge transfer less charge than methyl adds to the guanine.In methylating A-T base pair isomers,when the methyl adds to atom of O2,O4,N3 in thymine,the atom of H3′transfer to N1 in adenine,so the increase of charge all exit in adenine.
In summary,the research of the isomerization and methylation of DNA elucidate the isomerization mechanism and the influences of methylating base pair on DNA damage.It is. important to understand deeply the nature of DNA damage process to explore further the conditions of influencing DNA damage and further to control and utilize the process of DNA damage.
本论文运用量子化学方法研究了嘧啶碱基和嘌呤碱基四种碱基的异构化过程和甲基化碱基对的结构和性质,从微观角度研究了异构化机理和烷基化机理。通过对这些机理的研究对DNA损伤过程有全面,深入的认识,从而可以为抑制不良损伤和利用、开发有利损伤奠定基础并提供理论指导。这在化学以及生命科学领域均具有重大理论和实际意义。
主要研究内容及结论归纳如下:
1.利用密度泛函方法,在B3LYP/6-311+G~(**)基组水平上对所有的嘧啶异构体,过渡态分别在气相和液相中进行几何结构全优化。DNA嘧啶碱基胞嘧啶和胸腺嘧啶的异构化过程可分为原子间的质子转移和N-H键围绕C=N双键旋转两类。其中在原子间质子转移过程中,形成关键部分为平面四元环的过渡态,该四元环与碱基骨架共平面。质子通过四元环发生原子间转移。当考虑溶剂化效应时,所有的平衡态在液相中的能量小于在气相中的能量。但是所有过程的活化能却都增高。说明溶剂化效应增加反应的势垒。在气相和液相中质子转移过程的活化能大于N-H旋转过程的活化能。在研究温度范围内,直接导致碱基损伤的异构化过程,即DNA嘧啶碱基正常构型的异构化过程均属于热力学上的非自发过程;由于异构化过程仅仅涉及一个质子的键合情况的变化或位置的移动,故其熵变均很小。若可以达到异构化平衡,胞嘧啶正常构型异构化平衡常数和异构化率较大;而胸腺嘧啶正常构型发生异构化的平衡常数很小,异构化率也较小。两种异构化过程的反应速率很低。当考虑溶剂化效应时,液相中的异构化的速率会降低。
2.利用密度泛函方法在B3LYP/6-311+G~(**)基组水平上对所有的嘌呤异构体,过渡态分别在气相和液相中进行几何结构全优化。嘌呤碱基的异构化过程也可以分为原子间的质子转移和N-H围绕C=N旋转两类。其异构化过程ADE1→ADE2,GUA1→GUA2,GUA3→GUA5和GUA3→GUA7属于两个N原子间质子转移过程,GUA1→GUA3属于N原子和O原子间的质子转移,所有质子转移过程的过渡态均包括一个新形成的平面四元环,该四元环与嘌呤碱基骨架共平面。在所有N-H键围绕N=C双键的旋转过程的过渡态中,平面CNH垂直于整个分子平面。质子转移过程与N-H旋转过程相比具有更高的反应能垒,更小的反应常数和平衡常数。当考虑溶剂化效应时,所有的平衡态在液相中的能量小于在气相中的能量,除了TS-G56和TS-G78在液相中活化能小于气相中的活化能外,其它过程液相中的活化能大于气相中的活化能。热力学分析表明,四个碱基的正常构型均是异构体中热力学最稳定的构型,直接导致嘌呤碱基正常构型变化的异构化过程均属于热力学上的非自发过程;在研究温度范围内,根据平衡常数得到的最大异构化率分别约为:腺嘌呤5×10~(-8);鸟嘌呤10~(-3)。可见,两个嘌呤碱基之间的平衡损伤比率有很大差别。由Guanine引起的碱基异构化多于由Adenine引起的异构化过程。
3.用密度泛函(DFT)理论方法在B3LYP/6-31+G(d,p)基组水平上对G-C及A-T碱基对甲基异构体进行结构优化和分裂能计算研究发现,从几何构型将甲基异构体分为两类:一类是甲基加成到未参与氢键的原子上,N7-meG-C,N3-meG-C,N3-meA-T和N7-meA-T依然保持碱基对的氢键形式和配对方式,在第一次复制过程中对碱基对损伤的影响较小。另一类为甲基加成到参与氢键形成的原子上。N1-meA-T,N3′-me T-A,O4′-me T-A,O2′-me T-A,N3′-meC-G和O2′-meC-G碱基对的氢键结合形式,配对方式都发生了变化。第一次复制过程中对碱基对损伤的影响较大。O6-meG-C例外,O6原子虽然参与了氢键的形成,但O6碱基对甲基化物并未改变碱基对的氢键形式和配对方式,对碱基对损伤的影响较小。
从分裂能上分析可得,除了O2′-meC-G结构外,由于甲基是供电子基,使碱基对生成异构体的分裂能增加。甲基加成到Guanine上形成异构体的稳定性大于加成到Cytosine上形成的异构体的稳定性。G-C碱基对甲基异构体中造成DNA损伤较大的异构体其稳定性较低。甲基加成到Thymine上形成异构体的稳定性大于加成到Adenine上形成的异构体的稳定性。A-T碱基对甲基异构体中造成DNA损伤较大的异构体其稳定性反而较高。从电荷分析可以得出,氢键键长和电荷的分布与碱基对的分裂能没有直接的关系。碱基氢键间存在电荷转移,甲基加成到Cytosine上时,电荷的转移小于甲基加成到鸟嘌呤上。对于A-T碱基对来说,由于加成到TO2,TO4和TN3位后THY中H3′原子都转移到ADE的N1原子上,所以生成物中的电荷的增加都在腺嘌呤ADE上。
总之,通过对DNA异构化、甲基化过程的理论研究,初步阐明了异构化过程的反应机制和甲基化碱基对对DNA的损伤。这些结果对深刻理解DNA化学损伤过程的本质,进一步探索影响DNA化学损伤的条件和控制DNA化学损伤过程具有一定的理论和实践意义。
The DNA damage means all kinds of the abnormal changes of DNA molecular structure. Including,the breakage and crosslinkage of double helical structure of DNA chain, isomerization,deamination alkylation of DNA base.Most of DNA damages can be repaired by the repair system in biology body,which is the foundation to maintain the genetic stability.The number of un-repaired DNA damages is thimbleful,but these un-repaired damages maybe produce very important influence on organism.In the replication process,DNA damage can lead to gene mutation and bring forth senescence,tumor and other diseases related to gene. Some DNA damages may be transmitted to filial generation,which is called gene mutation in genetics.Gene mutation can do organism a lot of harm,for example,it can induce cancer.On the other hand,it may endow the cell new function,and finally result in biological evolution. Moreover,the mutation induced artificially is the important approach to improve or create species,prevent or cure cancer and other diseases related to gene.Thus the research of DNA damage mechanism is a very important subject in life science.
In this dissertation,we studied the isomerization of pyrimidine and purine base and methylating of base pair with density functional theory(DFT)calculations.Our purposes are to shed light on the mechanistic details of isomerization and methylation of DNA damage.The research of occurring and developing mechanism of DNA damage is the basis of utilizing advantageous damage and inhibiting disadvantageous damages.So it is very important research topic in biology and chemistry.
The valuable results in this dissertation can be summarized as follows:
The mechanism of DNA damage caused by the isomerization of pyrimidine base has been systematically studied by performing density functional theory calculations at the B3LYP/6-311+G(d,p)level.It is shown that the isomerizations of pyrimidine base can be classified into two types.The first is the hydrogen transfer between atoms,whose transition state includes a four-member ring.The second is the bond N-H rotation about the double bond N=C,and the plane CNH is perpendicular to the molecular plane in its transition state.The hydrogen transfer has higher reaction potential barrier,larger tunnel effect,and smaller equilibrium constant and rate constant than that of the N-H rotation.When the effects of hydration are considered in the framework of the polarizable continuum model,the two types of isomerizations will all have larger reaction barrier,larger tunnel effect and smaller rate of constant.The isomerizations leading directly to DNA damage are endothermic reaction and thermodynamic nonspontaneous processes.The DNA damage rate caused by the self-isomerization of cytosine and thymine is very slow.The probability of DNA damage caused by the cytosine isomerization is larger than that by the thymine.
The mechanism of DNA damage caused by the isomerization of purine base is studied with density functional theory calculations at the B3LYP/6-311+G(d,p)level.The transition states of all the isomerizations are obtained,and the intrinsic reaction coordinate(IRC) analyses are performed to identify these transition states further.The isomerizations of purine bases can be classified into two types.The first is the hydrogen transfer between atoms,whose transition state includes a four-member ring.The second is the bond N-H rotation about the double bond N=C,and the plane CNH is perpendicular to the molecular plane in its transition state.The hydrogen transfer has higher reaction potential barrier,larger tunnel effect,and smaller equilibrium constant and rate constant than that of the N-H rotation.Effects of the hydration are considered in the framework of the polarizable continuum model(PCM)in SCRF method at the B3LYP/6-311+G(d,p)level.The isomerizations which result in the configuration changes of purine base and bring directly the DNA damage are endothermic and thermodynamic non-spontaneous process.The probability of DNA damage caused by the guanine isomerization is larger than that by adenine.
Methylation of Watson-Crick adenine-thymine(A-T)and guanine-cytosine(G-C)base pair have been investigated by density functional theory calculations at the B3LYP/6-3 l+G(d,p) level.Calculations show that the 11 methyl isomers may be divided into two groups.(1)The methyl adds to an atom that is directly related to the hydrogen bonds of the base pair.(2)The methyl atom adds to an atom that is away from the hydrogen bonds of the base pair.In the fist group,N7-meG-C,N3-meG-C,N3-meA-T and N7-meA-T maintaining the planar structure of base pair have less influence on base pair damage.In the second group,N1-meA-T,N3′-me T-A,O4′-me T-A,O2′-me T-A,N3′-meC-G and O2′-meC-G which changes base pairing sequence,may cause a major lesion of DNA.
Except O2′-meC-G,the base pairing energy of other isomers are increase because the methyl is donor group.Isomers of methylating guanine are more stable than the isomer of methylating cytosine.Isomers of methylating thymine are more stable than isomer of methylating adenine.There is no direct relationship between the charge distribution and the stabilization energy.Charge transfer exists in base pair,when the methyl adds to the cytosine, charge transfer less charge than methyl adds to the guanine.In methylating A-T base pair isomers,when the methyl adds to atom of O2,O4,N3 in thymine,the atom of H3′transfer to N1 in adenine,so the increase of charge all exit in adenine.
In summary,the research of the isomerization and methylation of DNA elucidate the isomerization mechanism and the influences of methylating base pair on DNA damage.It is. important to understand deeply the nature of DNA damage process to explore further the conditions of influencing DNA damage and further to control and utilize the process of DNA damage.
引文
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