核酸碱基的非谐性振动:Ⅲ,DNA叠加二聚体的一维和二维红外光谱

用量子化学计算方法研究了DNA碱基单体及其15个B型和2个G-四链体的叠加二聚体的非谐性振动光谱特征.研究发现,从碱基单体到二聚体,C=O伸缩模式之间的相互作用很强,表现在其非谐性振动频率和非谐性常数都发生了明显的改变,特别是在含碱基G的叠加体中.这些变化能在一维和二维红外光谱中很好地表现出来.利用振动模式的势能分布和非谐性常数的组成分析,讨论了叠加二聚体中C=O模式的离域化程度.     

Fapy-G对碱基氢键复合物影响的理论研究

应用量子化学方法对2,6-二氨基-4-羟基-5-甲酰胺嘧啶(Fapy-G)与正常碱基作用形成的20种氧化碱基对的多种性质进行了理论分析,碱基G的C8位被氧化后N7和N9位分别增加一个H原子,使其由氢键受体变成氢键供体,N7,N9及O6原子所带的电荷变负,同时O6作为氢键受体的能力增强.与碱基单体相比,碱基对中形成氢键的受体原子所带的电荷平均减小0.05 e;供体H原子所带的电荷平均增大0.02 e.Fapy-G分子中六元环上受体N原子参与形成氢键时,环的呼吸振动模式和N与对位C的振动模式的振动频率蓝移;与氢键相关的振动频率红移.所有氧化碱基对中,NH…N比NH…O氢键作用更强,且在NH…N氢键中,在六元环上的供体N原子形成的氢键比在氨基或开环上的供体N原子形成的氢键强.Fapy-G与碱基A作用结合能区域顺序为1>2>4>3,与碱基T(R)作用区域顺序为3=4>1>2;水溶液使Fapy-G与碱基C作用的结合能减弱程度最大,结合能达到41.84~58.58 k J/mol,且使碱基对结合能力次序发生改变.     

铂配合物与DNA碱基对间相互作用的理论研究

用量子化学方法研究一系列Pt(II)配合物作用于嘌呤碱基N7位点后对Watson-Crick碱基对AT、GC的影响. 计算结果显示铂配体与碱基对AT、GC的作用以静电作用为主，同时极化作用也是影响GC碱基对的重要因素. 静电作用极大地增强了铂化嘌呤碱基与嘧啶碱基间的相互作用，而嘌呤碱基与嘧啶碱基间作用与未铂化碱基对作用相近. Pd(II) 和 Ni(II)的相关研究得到类似的结果. 碱基对间氢键作用“二阶微扰能”分析结果与氢键强弱变化一致.     

7,8-二氢-8-氧鸟嘌呤碱基对的量子化学研究

遗传信息的完整性不断受氧化基因的威胁,7,8-二氢-8-氧鸟嘌呤（8-oxo-G）是氧化DNA损伤最常见的产物. 氧化碱基会引起基因突变、癌变及衰老等. 应用量子化学方法分析得出：鸟嘌呤（G）被氧化为8-oxo-G后,其电荷分布、氢键的供体和受体位点的数目和位置随之改变,N7和O6原子所带的电荷变得更负,使得它们作为氢键供体的能力增强. 从而G被误认为其他碱基,与正常碱基形成多种氢键复合物. 可将8-oxo-G划分为3个作用位点与正常碱基相互作用. 与正常的单体相比,碱基对中形成氢键的受体原子上所带电荷平均变负0.05e,占原电荷的8%; 供体H原子所带电荷平均变正0.02e,占原电荷的4%. 1位点与正常碱基作用形成的氢键复合物更稳定,2位点和3位点性质相似,水溶剂使碱基对的结合能力减弱,其中与C作用形成氢键复合物的结合能减弱程度最大,且使碱基对结合能力的次序改变. 在8-oxo-G导致的GC→TA突变中,亲核反应位点从G所在链转到A（C）所在链,影响酶对碱基的识别,从而产生基因突变.     

DNA甲基化-非甲基化碱基间堆积作用的理论研究

运用二级Mфller-Plesset(MP2)理论方法和cc-pVDZ基组优化了6-甲基鸟嘌呤(O6-MethylG),4-甲基胸腺嘧啶(O4-MethylT)以及5-甲基胞嘧啶(C5-MethylC)与DNA碱基鸟嘌呤(G),腺嘌呤(A),胞嘧啶(C),胸腺嘧啶(T)之间的堆积构型.在MP2/aug-cc-pVXZ//MP2/cc-pVDZ(X=D,T)水平上,采用完全基组外推方法校正了堆积碱基对间的相互作用能,并用完全均衡校正法(CP)校正了基组重叠误差(BSSE).MP2计算结果表明,DNA碱基甲基化使得嘧啶-嘧啶、嘧啶-嘌呤堆积碱基间的平行旋转角发生明显改变,并使堆积碱基间的相互作用能增大.在MP2/cc-pVDZ计算级别上得到了各堆积碱基对的全电子波函数,并用分子中的原子理论(AIM)分析了堆积碱基对间的弱相互作用.AIM分析结果显示,甲基化增强了堆积碱基间的π-π作用,且甲基氢与相邻碱基间形成H2CH…X(X=O,N,CH3,NH2)等类型的氢键.甲基化损伤使碱基间重叠程度增大、π-π作用增强以及堆积碱基间形成多个氢键,是堆积作用能增加的主要原因.     

致癌有机化合物分子片段致癌机理的研究

以有机物的分子连接性指数和微扰分子轨道指数作结构、能量参数,从分析致癌有机物分子片段与生物遗传基因DNA链互补碱基对发生共价交联的构效角度出发,首次得出产生碱基移码型或碱基置换型化学致癌的主要过程是化合物分子片段中活性原子与DNA互补碱基对间氢键的共价结合,显示致癌活性的充分必要条件是碱基对G≡C间有两个氢键与致癌分子片段发生特异交联.对100余种已知致癌物的致癌分子片段进行计算分析,成功地获得了有机物分子片段定量结构-致癌活性的估测模式.     

镍离子(Ⅱ)印迹聚合物的制备及性能研究

以镍(Ⅱ)离子为模板,丙烯酰胺为功能单体,二乙烯基苯为交联剂,偶氮二异丁腈为引发剂,甲醇为溶剂,采用本体聚合法制备了镍离子(Ⅱ)印迹聚合物.用红外光谱对镍离子印迹聚合物的结构进行表征,红外光谱研究表明聚合物中存在与模板分子相互作用的特征基团.通过研究Ni2+与单体的物质的量之比、单体与交联剂的物质的量之比、溶剂量对镍离...     

复合酸掺杂导电聚苯胺的性能研究

以苯胺为单体、过硫酸胺为氧化剂,由化学氧化聚合法在磺基水杨酸和硫酸的复合酸的水溶液中合成导电聚苯胺,并通过压片法、激光粒度分析、扫描电镜、差热分析及红外光谱对掺杂态聚苯胺的电导率、表面形貌及结构进行了研究.结果表明,复合酸掺杂聚苯胺的热稳定性比仅用硫酸掺杂聚苯胺的有了很大的提高;所得导电聚苯胺的粒度分布比较均匀(平均粒径约15.4μm);复合酸掺杂使聚苯胺分子链上的电荷呈离域化,掺杂程度提高.     

DNA碱基(对)及其Zn2+复合物对CO2,N2,H2小分子的吸附

用M062X/6-31+G^*方法探讨了腺嘌呤(A)、 胸腺嘧啶(T)、 鸟嘌呤(G)、 胞嘧啶(C)及其碱基对(AT, GC)以及Zn²⁺复合物(AAA-Zn²⁺, AAT-Zn²⁺和GGC-Zn²⁺)对混合小分子H₂, N₂, CO₂的吸附情况, 系统研究了其相互作用模式及吸附强度, 预测了常见混合气体分子与碱基(对)及复合物的吸附位置. 研究表明, CO₂倾向于以氢键的形式结合到碱基(对)的氨基氢或亚氨基氢上, 而N₂和H₂分子则倾向于结合到这些碱基(对)的平面π电子上, 以堆垛的形式存在. 根据吸附强度大小, 预测了由这些碱基为骨架合成的金属有机骨架(MOF)吸附材料对小分子的选择性吸附顺序为H₂22. 研究表明, 以AT对结合金属Zn²⁺为节点的纯天然碱基对构成的MOF要比实验合成的AA碱基对与Zn²⁺结合的MOF具备更好的吸附和分离性能.     

苯乙烯基氮氧杂芳烃间的交叉光二聚反应

用中压汞灯(λ > 300 nm)照射4-苯乙烯基吡啶、2-苯乙烯基苯并噁唑和5-苯基-2-苯乙烯基噁唑三种杂芳基乙烯单体中任意两种的硫酸水溶液，得到三种交叉二聚体.用高效液相色谱跟踪研究了交叉光二聚反应，发现每组反应生成三种光二聚体，其中二种为单体自身的光二聚体，而另外一种是两种不同单体的交叉光二聚体.交叉二聚体通过柱色谱分离得到，其顺式头对尾结构经紫外、红外、氢谱、碳谱和元素分析确定.用紫外光谱和高效液相色谱跟踪研究了交叉光二聚体的稀溶液在低压汞灯（λmax=254 nm）照射下的光解反应.研究发现交叉二聚体能够彻底发生光解，首先生成原来的反式单体，所生成的反式单体容易发生异构化而生成顺式单体，最终建立起反顺异构化平衡.     

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Evolution of Artificial Base Pairs with Hydrogen Bond Complementarity

Artificial base pairs,from the perspective of synthetic biology,are designed to contain the features of modularity,orthogonality,and manipulability.And the development of artificial base pairs has beat endowed with responsibility to understand the biological process,improve the recognition capacity and stability of aptamers,and develop the nucleoside drugs,diagnosis,and drag delivery.In this review,we first gave a concise introduction of artificial base pairs based on their interaction modes including alternative hydrogen bonding,hydrophobic interaction,and metal coordination.Then we displayed the detailed information of artificial base pairs with hydrogen bonding interaction,and analyzed how the changes of their structures affect their functions.Subsequently,we highlighted the applications of functional artificial base pairs in aptamer discovery,diagnosis,and drug delivery.Finally,an insight into the remaining challenges and future perspective of the artificial bases was provided.     

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

DNA vibrational coupling revealed with two-dimensional infrared spectroscopy: insight into why vibrational spectroscopy is sensitive to DNA structure

Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.     

Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

Changes of molecular structure and associated charge distributions, and changes of anharmonic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH2, N H, and C=O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results reveal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases.     

Vibrational dynamics of DNA: IV. Vibrational spectroscopic characteristics of A-, B-, and Z-form DNA's

Linear and nonlinear IR spectroscopic studies of nucleic acids can provide crucial information on solution conformations of DNA double helix and its complex with other molecules. Carrying out density functional theory calculations of A-, B-, and Z-form DNA's, the authors obtained vibrational spectroscopic properties as well as coupling constants between different basis modes. The vibrational couplings that determine the extent of exciton delocalization are strongly dependent on DNA conformation mainly because the interlayer distance between two neighboring base pairs changes with respect to the DNA conformation. The Z-DNA has comparatively small interlayer vibrational coupling constants so that its vibrational spectrum depends little on the number of base pairs, whereas the A-DNA shows a notable dependency on the size. Furthermore, it is shown that a few distinctively different line shape changes in both IR and two-dimensional IR spectra as the DNA conformation changes from B to A or from B to Z can be used as marker bands and characteristic features distinguishing different DNA conformations.     

5‐Mercuricytosine: An Organometallic Janus Nucleobase

The base‐pairing properties of 5‐mercuricytosine have been explored at the monomer level by NMR titrations and at the oligonucleotide level by melting temperature measurements. The NMR studies revealed a relatively high affinity for guanine, hypoxanthine, and uridine, that is, bases that are deprotonated upon coordination of Hg^II. Within an oligonucleotide duplex, 5‐mercuricytosine formed Hg^II‐mediated base pairs with thymine and guanine. In the former case, the duplex formed was as stable as the respective duplex comprising solely Watson–Crick base pairs. Based on detailed thermodynamic analysis of the melting curves, the stabilization by the Hg^II‐mediated base pairs may be attributed to a comparatively low entropic penalty of hybridization.     

Nuclear quantum effect and temperature dependency on the hydrogen‐bonded structure of base pairs

The structure of Watson–Crick‐type adenine‐thymine and guanine‐cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6‐DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen‐bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen‐bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen‐bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two‐dimensional free energy landscape along Buckle and Propeller modes. © 2013 Wiley Periodicals, Inc.