与DNA相关的鸟嘌呤及其衍生物性质和作用机理研究

英文题名：Studies on the Properties and Functional Mechanisms of Guanine and Its Derivatives Associated with the DNA
作者：孙立祥
论文级别：博士
学科专业名称：物理化学
中文关键词：鸟嘌呤 ; 碱基对 ; 单电子氧化 ; 质子转移 ; 空穴转移
英文关键词：Guanine ; Base pair ; One-electron oxidation ; Proton transfer ; Hole transfer
学位年度：2007
导师：步宇翔
学科代码：070304
学位授予单位：山东大学
论文提交日期：2007-04-16

摘要

鸟嘌呤(G)是组成DNA的四种碱基之一，具有4种DNA碱基中最小的绝热电离势，所以DNA的氧化通常发生在鸟嘌呤碱基上。他们都具有N和O等活性位，可以结合成碱基对，并且由于DNA双螺旋大沟与小沟的存在，使得外界因素可以影响碱基对的结构性质。本文重点讨论了金属离子、单电子氧化、质子离解、质子转移等众多不同的因素对鸟嘌呤及其鸟嘌呤-胞嘧啶碱基对的氢键性质和配对能力的影响，进而探讨DNA成功的保守复制和碱基错配形成的影响因素以及碱基错配的后果，从而逐步达到揭示生命奥秘的目的。取得的一些有意义的研究成果，具体如下：
     一、对GC碱基对离解能和氢键的性质的认识是理解碱基对生理功能的基础。单电子氧化和Li~+离子的耦合可以增强GC碱基对中鸟嘌呤和胞嘧啶之间的相互作用。Li~+离子和鸟嘌呤的相互作用是相互吸引，并且是引起GC碱基对中氢键极化而增强GC相互作用的原因。GC阳离子和Li-GC阳离子中三个氢键的协同作用与中性GC碱基对内的三个氢键的协同作用不同。在GC碱基对阳离子和Li-GC阳离子中可以发生从鸟嘌呤的N1原子到胞嘧啶的N3原子之间的质子转移过程。过渡态的构型是一个非平面结构，尤其是Li-GC阳离子的过渡态。对质子转移过程的活化能分析表明GC~+阳离子的质子转移前和质子转移后的构型能在气相中同时存在，但是对于Li-GC~+体系，没有质子转移的构型是气相中的主要物种。
     二、在GC碱基对阳离子研究的基础上，考察了在碱基上增加2′-脱氧核糖对碱基对的各种性质的影响。一个电子从核酸对dGdC上电离会引起三个氢键长度的显著变化，氢键O…H4-N4的长度增加了0.160(?)，氢键N1-H1…N3的长度和N2-H2…O2氢键的长度分别缩短了0.116(?)和1.234(?)为了揭示在单个的碱基上增加糖环后绝热电离势(AIP)的真实趋势，我们计算了核酸对dGdC的绝热电离势。依据结构的变化，能量的变化和电荷分布情况探讨了注入一个正电荷的后果。预测到核酸对dGdC的绝热电离势是一个正值，为6.48eV，并且相对于碱基鸟嘌呤和胞嘧啶以及碱基对GC的绝热电离势有一个大幅度的下降。配对与增加糖环对绝热电离势的作用可以看作是各自作用的总和。配对对鸟嘌呤绝热电离势的影响和增加糖环对鸟嘌呤绝热电离势的影响差不多。在dGdC~+核酸对阳离子中单电荷主要位于脱氧核糖鸟嘌呤分子片上。dGdC~+核酸对阳离子负的垂直电子结合能(-5.98eV)表明阳离子状态相对于其垂直结合电子的状态是一个不稳定的状态。对于中性的dGdC核酸对预测到一个相当大的垂直电离势(VIP 7.05eV)。在GC碱基对阳离子和dGdC核酸对阳离子中可以发生从鸟嘌呤的N1原子到胞嘧啶的N3原子的质子转移过程，并且这个过程因为糖环在碱基上的连接而变得容易。因此，可以推测质子转移前和质子转移后的dGdC核酸对阳离子能同时存在。
     三、对G-M(M=Li，Na)阳离子的N1-H质子离解能随水分子结合数目和结合模式的变化进行了考察。当水合M~+离子与鸟嘌呤结合时有三种模式：NO模式、N模式和O模式。水合M~+离子与鸟嘌呤的结合能随着水分子数目的增加而降低。在不同数目的水分子和不同的水分子结合模式结合到G-M~+离子的条件下我们计算了G-M~+复合物的质子离解能。结果显示三种不同模式之间的质子离解能差别很小，并且Na~+复合物的质子离解能稍大于Li~+复合物的质子离解能。水分子结合到M~+离子上对N1-H质子的离解作用很小，但是当水分子结合到N1-H质子上并且作为水合质子离解的时候，水分子的作用就很大。振动频率分析显示振动频率的变化对应着结构的变化和N1-H质子离解能的变化。在生理条件下，鸟嘌呤的N1-H质子比较容易失去，质子离解能为45-60 kcal／mol。
     四、鸟嘌呤的电离对碱基对形成的作用和鸟嘌呤的电离对DNA内空穴转移的作用和鸟嘌呤阳离子的去质子化对碱基对形成的作用都进行了研究。与中性的DNA碱基配对可以降低鸟嘌呤的绝热电离势，而与质子化的DNA碱基配对则可以升高鸟嘌呤的绝热电离势。Watson-Crick模式的碱基对的绝热电离势的降低对空穴转移的作用很小，但是由于碱基错配引起的结构的变化会打破DNA螺旋的π-堆积结构，从而会不利于空穴的转移。错配的碱基对GA-1和GA-2可以增加空穴从一条链转移到另一条链上的可能性。质子化的腺嘌呤、胸腺嘧啶、胞嘧啶以及中性的鸟嘌呤与鸟嘌呤通过Hoogsteen模式配对以后对空穴的转移有很大的影响，但是影响的机理却不尽相同。质子化的腺嘌呤、胸腺嘧啶、胞嘧啶通过Hoogsteen模式与鸟嘌呤配对以后，鸟嘌呤的绝热电离势会大大增加，从而阻止空穴的转移。当中性的鸟嘌呤通过Hoogsteen模式与鸟嘌呤配对以后，鸟嘌呤的绝热电离势会大大降低，因此空穴会自发地转移到第三条链上并被Hoogsteen模式的GG碱基对所捕获。从能量的观点看，鸟嘌呤的电离不会增加Watson-Crick模式碱基对错配的几率，但是鸟嘌呤阳离子上的质子失去会有利于G(-H)·与鸟嘌呤的结合。在Hoogsteen模式的碱基对中，鸟嘌呤的电离对作用模式的作用很小。但是当质子化的腺嘌呤、胸腺嘧啶、胞嘧啶通过Hoogsteen模式与鸟嘌呤配对可能会因为鸟嘌呤的电离而离解。质子从鸟嘌呤阳离子上失去对Hoogsteen模式碱基对的成对能影响很小。
     五、通过dGTP结合到DNA模版的过程研究了DNA保守合成的机理。从DNA碱基上切除水分可以增加正确的碱基对和不正确的碱基对之间的能量差，但是水分子对形成吉布斯自由能的影响依赖于水分子的结合位点。从即将进入的dNTP上切除水分子的作用不是DNA成功复制的唯一因素而是DNA成功复制的第一步。第二步是DNA聚合酶通过比较正确的碱基对和不正确的碱基之间的结构比较来选择正确的DNA碱基。精氨酸668(Arg668)在即将进入的dNTP上的结合可以降低碱基对的形成吉布斯自由能，尤其是对于正确的碱基对，因此增加DNA形成的速率。当DNA末端的底物是正确的碱基，鸟嘌呤和腺嘌呤的延伸比胞嘧啶和胸腺嘧啶的延伸要快的多。因为当DNA末端的碱基是鸟嘌呤和腺嘌呤时，精氨酸668可以和底物末端的小沟以及即将进入的dNTP的糖分子片上的环氧之间形成一个氢键叉。因为不正确的碱基对的结构和正确的碱基对的结构有一些差别，DNA聚合酶对不正确的碱基对的延伸所起的作用小于对正确的碱基对延伸所起的作用。错配的碱基对的延伸速率将小于正确的碱基对的延伸速率。不正确的碱基对的延伸速率的降低使得核算外切酶有机会发挥活性切除不正确的碱基对。精氨酸668不能像阻止GC碱基对和GA、GG错配碱基对的延伸那样阻止GT碱基对的延伸。这也许是因为GT碱基对的结构与正确的碱基对AT的结构仅有微小的差别。
Guanine (G) is one of the primary components of the DNA, with the lowest oxidation potential among four DNA bases, so the oxidation in DNA damage is predicted to be produced at this site. They have several active sites, such as N and O, which incarnate the effects from the outer factors on its structures and properties. Thus, in the present dissertation, the effects of various outer factors, such as metal ions, oxidation, deprotonation, proton transfer etc. on the hydrogen bond character and the ability of the paring of the guanine and GC base pair have been investigated in detail. On the basis of the prevenient studies, the influencing factors of the fidelity synthesis of DNA and the formation of the mispairs have been investigated, then the aim to reveal the secret of life can be carry out step by step. Some significant progresses have been made, which can be described as follows.
     1. The cognition on the dissociation energy and H-bond character of G-C cation and Li-GC cation is the basis to understand the biological function. The one electron oxidation and the coupling of Li~+ to guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li~+ with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations are different from that in the neutral GC base pair. The proton transfer process of between N_1 of the guanine and N_3 of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out-of-plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton transfer process shows that the GC~+ before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC~+ system, the Li-GC~+ without proton transfer is the dominating species in the gas phase.
     2. On the basis of the results of the GC cation, the effect of the addition of the sugar moiety on the character of the GC base pair has been investigated. The ionization of an electron from dGdC results in remarkable changes to the three hydrogen bonding distances, the O…H4-N4 distance increased by 0.160 A and the N1-H1…N3 distance and the N2-H2…O2 distance decreasing by 0.116 A and 1.234 A, respectively. The ionization potential of the dGdC pair was studied to reveal the correct trends of adiabatic ionization potential (AIP) under the influence of the additional components to the individual bases. The consequence of positive charge in terms of structural variations, energetic changes, and charge distribution were explored. The AIP of dGdC is predicted to be positive (6.48 eV), and it exhibits a substantial increase compared with those of the corresponding bases G and C and the nucleic acid base pair GC. The effects of pairing and the addition of the sugar moiety on the AIP are well described as the summation of the individual influences. The influence of the pairing on the G is comparable to that of the addition of 2-deoxyribose. The singlet charge is mainly located on the deoxyriboguanosine moiety in the cationic dGdC pair. The negative vertical electron attachment energy (-5.98 eV) for dGdC~+ suggests the cationic state is unstable with respect to electron attachment vertically. A large vertical ionization potential (VIP 7.05 eV) has been determined for the neutral dGdC nucleoside pair. The proton-transfer process between N1 of the guanine and N3 of the cytosine can occur in the GC cation and dGdC cation, and this process becomes easier when the sugar moiety linked on the base pair. Therefore, one may expect that the cationic dGdC nucleoside pair before and after proton transfer should be exist simultaneously.
     3. The variation of N1-H proton release energy of G-M (M=Li, Na) cation have been investigated. There are three modes (NO mode, N mode and O mode) when the hydrated-M~+ bonds to guanine. The bonding energy of the hydrated M~+ to the guanine reduces following the increase of the number of the water molecule. The proton release energies of the G-M~+ complexes are calculated at the condition of the different numbers of the water molecules and the different modes of the water molecules bonded on the G-M~+. The results show that the difference of the proton release energy on three modes is very small, and the proton release energies of the Na~+ complexes are slightly larger than that of the Li~+ complexes. The effect of the water molecules bonded on the M~+ cation on the N1-H proton release is very small, but the effect is very large when the water molecules bond on the N1-H proton and the proton release as the hydrated proton. The vibrational frequency analysis shows that the changes of the vibrational frequency are consistent with the changes of the geometry and the changes of the N1-H proton release energy. The N1-H proton release (N1-H proton release energy: 45-60 kcal/mol) of the guanine can occur easily at the condition of the biology system.
     4. The effect of the ionization of the guanine and the deprotonation of the guanine cation on the formations of base pairs and on the hole transfer in DNA was explored. The base pairing with neutral DNA base lowers the adiabatic ionization potential of guanine, while the base pairing with protonated DNA base heightens the ionization potential of guanine. The lower of the adiabatic ionization potential of guanine in Watson-Crick mode base pairs has a slight effect on the hole transfer, but the structural changes resulted from the DNA base mispair may break theπ-stack in DNA helix, thus make against the hole transfer. The mispairs GA-1 and GA-2 increase the probability of the hole transfer from one strand to other strand. The protonated A, T, C and neutral G pairing with guanine through Hoogsteen mode may significantly affect on the hole transfer, but the mechanisms are different from each other. When the protonated A, T or C base pairs with guanine through Hoogsteen mode, the ionization potential of guanine has been increased and thus the hole transfer may be stopped. While the neutral guanine pairs with guanine through Hoogsteen mode, the ionization potential of guanine has been decreased significantly and thus the hole can spontaneously transfer to the third strand and can be trapped by the Hoogsteen base pair GG when the hole transfer along the DNA helix. In the view of the energy, the one electron ionization of guanine can not result in the Watson-Crick mispair of DNA base pair, but the deprotonation from the guanine cation is in favor of the combination of the G(-H) and guanine. In the Hoogsteen base pairs. the one electron ionization of guanine affects slightly on the interaction mode, but it may result in the dissociation of the Hoogsteen base pair if the DNA bases pairing with guanine are the protonated A, T and C. Dehydrogen from guanine affects slightly on the hydrogen bonding energy of the Hoogsteen base pairs.
     5. The mechanism of the fidelity synthesis of DNA associated with the process of the dGTP combination to the DNA template was explored. The excluding of water molecules from the hydrated DNA bases can amplify the energy difference between the correct and incorrect base pairs, but the effect of the water molecules on the Gibbs free energy of formation is dependent on the binding sites for the water molecules. The water detachment from the incoming dNTP is not the only factor but the first step for the successful replication of DNA. The second step is the selection of the DNA polymerase on the DNA base pair through the comparison between the correct DNA base and the incorrect DNA base. The bonding of the Arg668 with the incoming dNTP can enlarge the Gibbs free energies of formation of the base pairs, especially the correct base pairs, thus increase the driving force of the DNA formation. When the DNA base of the primer terminus is correct, the extension of the guanine and the adenine is quicker than that of the cytosine and the thymine because of the hydrogen bonding fork formation of Arg668 with the minor groove of the primer terminus and the ring oxygen of the deoxyribose moiety of the incoming dNTP. Due to the geometry differences of the incorrect base pairs with the correct base pairs, the effect from the DNA polymerase is smaller on the incorrect base pair than on the correct base pair, and the extension of a mispair is slower than that of a correct base pair. This decreases the extension rate of the base pair, and thus allows a proofreading exonuclease activity to excise the incorrect base pair. Arg668 can not prevent the extension of G/T mispair as well as the G/C correct base pair and G/A, G/G mispairs. This may be attributed to the small geometry difference between the G/T base pair and the correct A/T base pair.

引文

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