不同波段的紫外辐射对DNA构象影响的拉曼光谱研究

研究了小牛胸腺DNA水溶液经不同时问不同波段紫外辐射后的拉曼光谱。结果表明：仅仅经过9min强度为18．68W／m^2。的全波段紫外辐射,DNA就遭到了严重损伤：表征PO2^-对称伸张振动的1094cm^-1谱线分裂成4条谱线．说明DNA构象遭到破坏,构型发生了变化。UV—A＆UV—B波段的紫外辐射对DNA的影响比全波段的紫外辐射对DNA的影响小得多,但经过较长时间辐射后,仍对DNA构型构象产生了影响,即A型构象增强,B型构象减弱．经过2h的UV—A辐射,出现了表征A型构象的805cm^-1和816cm^-1谱线,且816cm^-1峰与未经辐射的表征A型的803cm^-1峰相比,强度大得多。经过16h的UV—A辐射后,805cm^-1谱线消失,816cm^-1谱线移到了813cm^-1,且强度减弱50％,表明水溶液中的DNA在UV—A照射中A型构象不稳定,处于变化之中。     

三链DNA |dA10 2DT10的近红外付立叶拉曼光谱

最近通过核磁共振、振动光谱和分子力学模拟研究表明,在溶液中三螺旋DNA的构象具有一定程度的复杂性和多样性．本文首次采用近红外付立叶拉曼光谱研究了三螺旋DNA dA10•2d10和相应的双螺旋DNA dA10•dT10在溶液中的构象．结果表明该三螺旋DNA同时存在C3’－内褶／反对称（A－型）和C2’－内褶／反对称（B－型）两种构象,而且在823cm－1处的较强谱带暗示还存在一种处于A和B构型之间的中间构型．对出现在1218cm-1和638cm-1处、归属于对糖环构象敏感的胸腺嘧啶残基的两个特征谱带进行分析,获得了除C2’－内褶构象外其它构型存在的证据．另外,双螺旋DNA的FT－Raman光谱表明该双螺旋DNA在溶液中以A－和B－两种构型共存．     

Loop环对分子内三螺旋DNA稳定性的影响

用分子力学方法研究了 4个分子内三螺旋DNA ( 5′ d(TC) 6 d(T) m d(CT) 6 d(C) n d(AG) 6,m ,n分别为 4,3)的稳定性 ,并与相应的分子间三螺旋d(TC) 6 d(AG) 6·d(CT) 6进行了比较 .结果表明 :Loop环对分子内三螺旋的稳定性影响较小 ,但是Loop上碱基和糖环构象的变化依赖于Loop环的长度 .Loop使分子内三螺旋DNA嘌呤链的碱基堆积作用降低 ,链长增加 .三螺旋DNA的糖环构象大部分是S型 ,同时也存在N型以及其他构象 .     

氯乙基亚硝基脲烷化碱基导致DNA单链断裂的机理研究

采用密度泛函理论(DFT)和MΦller-Pleset微扰理论(MP)方法对氯乙基亚硝基脲(CENUs)烷化DNA碱基导致单链断裂的机理进行了研究. 对包括CENUs的分解、DNA碱基的烷化、糖苷键的水解、脱嘌呤位点的开环以及最终导致单链断裂的磷酸二酯的消除在内的多步反应过程进行了探讨. 在B3LYP/6-31++G**水平上对各驻点(反应物、中间体、过渡态和生成物)进行了全几何结构优化; 为了模拟细胞环境, 采用自洽场连续极化模型(CPCM)在相同计算水平上对各驻点进行了水相中的单点能计算或全几何结构优化. 分别在B3LYP/6-31++G**和MP2/6-311++G**水平上绘出反应势能曲线, 结果显示, 在整个反应过程中, 磷酸二酯的消除反应能垒最高, 而氯乙基重氮盐离子烷化DNA碱基的反应能垒最低. 理论分析结果表明, CENUs 一旦分解便很容易烷化DNA碱基, 随后生成的氯乙基化鸟嘌呤会迅速从DNA链上脱去, 尽管如此, 脱嘌呤位点最终导致DNA单链断裂的一系列反应则是一个缓慢的过程, 这与断链反应的动力学实验结果相符合.     

后处理过程中以水为溶剂的干法纺再生丝素纤维的结构演变

以水为溶剂的干法纺再生丝素蛋白纤维可通过后处理提高其力学性能,且后处理方法对纤维性能的提高程度有很大影响。为了优化干法纺再生丝素蛋白纤维的后处理工艺,定量研究了两种后处理方法中再生丝素蛋白分子的取向结构和构象演变,即方法A(纤维先在φ=80%的乙醇水溶液中浸泡1 h,再在热蒸汽中拉伸2倍)与方法B(纤维先在φ=80%的乙醇水溶液中拉伸2倍,再在该溶液中浸泡1 h)。探讨了纤维结构变化与力学性能之间的关系。结果表明:在乙醇水溶液中或在热蒸汽中拉伸均比仅在乙醇水溶液中浸泡更有利于丝素蛋白的构象转变,也对提高丝素蛋白分子链的取向更为有效。与方法A相比,方法B更能提高纤维的取向程度、β-折叠构象的含量以及力学性能。     

DNA的~(13)C化学位移与其链间嘌呤-嘌呤碰撞的相关性

本文发现并间接证实了DNA的~(13)C化学位移与其结构参数(主轴螺旋扭曲角Ω,碱基平面滚动角ρ,主链扭曲角δ和螺旋浆式扭曲角ω)之间存在着相关性,文中阐明了与这些结构参数相关的碳及其理论上的解释。这些碳的化学位移相对变化明显地反映出DNA链间嘌呤-嘌呤碰撞(立体障碍)所引起的DNA双螺旋局部结构的变化,并与Calladine-Dickerson加和函数Σ作了比较。从DNA的~(13)C NMR谱可以得到有关其构象的信息,从而有可能通过~(13)C谱观测DNA在溶液中的Ω,ρ,δ和ω等结构参数。     

自组装DNA吸附取向的表面增强拉曼光谱法研究

对金基体上自组装寡聚核苷酸探针杂交前后进行电化学非现场及现场表面增强拉曼光谱(SERS)研究.非现场SERS研究表明,杂交形成的dsDNA在基体表面以A型和B型两种构象同时存在,杂交过程可能伴随DNA链在基体表面吸附取向的变化.根据现场SERS研究结果可知,ssDNA及dsDNA的大多数SERS谱带强度随电极电位正移而降低,尤其是归属于碱基A的两种面外振动模式,谱带变化更为明显.利用SERS表面选择定则判断出随着电极电位由负向正变化,ssDNA及dsDNA螺旋吸附取向由垂直吸附向平躺吸附于金基体表面变化.     

DNA脱碱基位点的检测方法及其生物学研究进展

DNA中糖苷键断裂形成的脱碱基位点（脱嘌呤/嘧啶位点,AP位点）是常见的DNA损伤类型之一,由核苷酸自发水解产生,也是DNA碱基切除修复途径中的关键中间体。若修复不及时,可能会导致DNA复制阻滞和DNA链断裂,产生突变和细胞毒性,同时还会引起形成DNA交联或DNA－蛋白质交联的损伤,因此对于AP损伤的检测有助于理解细胞氧化应激损伤和基因毒性物质的毒性评价。目前检测AP位点的方法有14C或32P后标记法、酶联免疫吸附分析（ELISA）法和液相色谱－质谱（LC－MS）技术等。该文重点概述DNA中AP位点的检测方法和生物学研究进展,并展望了AP位点损伤相关研究的前景。     

胰岛素A和B链相互作用的圆二色性研究

本文报道以圆二色性方法在相同条件下测得S-硫甲基型A链的α螺旋、β折迭的含量为15％及27％;B链为22％,23％;A和B链混合后为24％,26％。表明A和B链相混后肽链构象有一定调整,α螺旋含量有所增加。以还原型A及B链进行实验,也得到类似结果。加入二巯基苏糖醇明显减少A及B链的有序成分。上述结果表明胰岛素A及B链有一定二级结构;在能重组成胰岛素的最适条件下,A及B链相混后,因次级键相互作用,两肽链构象有一定调整,有序程度有所提高。     

固态磷脂相变行为的红外和拉曼光谱研究

用红外和拉曼光谱方法在２９０～４０５Ｋ的温度范围内考察了无水二肉豆蔻酰磷脂酰乙醇胺的分子构象随温度的变化。结果表明，该磷脂在３６５Ｋ附近的熔化相变过程中，不仅酰链的构象和堆积发生了有序－无序转变，而且极性头部基团和接界区域基团也发生了结构重排；逆相变过程中，烷基链构象重新恢复了有序，但头部基团和甘油骨架构象没有恢复原始有序状态。     

DNA碱基激光拉曼光谱检测方法的研究

以激光拉曼光谱仪采集腺嘌呤(A)、鸟嘌呤(G)、胞嘧啶(C)、胸腺嘧啶(T)的拉曼光谱图,分析了各碱基谱峰归属,并依据归属结果检测混合碱基组成。结果显示:4种碱基的特征峰集中在175～1 800cm~(-1)。相同积分时间和激光功率条件下,该波段内嘌呤碱基的激光拉曼光谱峰高于嘧啶碱基的谱峰。腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶分别在723、648、791、1 368 cm~(-1)处的谱峰最强,利用这些特征峰能在2min内鉴别出混合碱基中的各碱基。     

BASE RELEASE FROM DNA AND POLYNUCLEOTIDES UPON 193 nm LASER EXCITATION

Release of bases form calf thymus DNA and three polynucleotides, induced by 20 ns excitation at 193 nm in aqueous solution at pH 7, was detected by HPLC. The quantum yields of formation of free bases (phi B) from double-stranded DNA (0.4 mM) are independent of intensity, indicating a one-quantum mechanism of N-glycosidic bond cleavage. The phi B values increase in the order guanine, thymine, adenine, cytosine, the latter being phi C approximately 7 x 10(-4) for double-stranded DNA under Ar and O2. The larger phi B values in N2O-saturated solution, e.g., phi C = 1.2 x 10(-3), are ascribed to additional base release via OH-adduct radicals. The phi B values of homopolynucleotides increase in the order poly(G), poly(A) and poly(C), e.g. phi C = 7 x 10(-3) under Ar, as do the efficiencies for base release per radical cation (eta B). A comparison of the eta B values with the efficiencies of single-strand breakage for poly(C), poly(A) and DNA shows a similar trend; both are markedly larger for pyrimidines than for purines. Pathways to undamaged bases, initiated from base radical cations, are proposed.     

Detection of Mercury-TpT Dinucleotide Binding by Raman Spectra: A Computational Study

The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.     

Studies on a New Usage of Hypophosphorous Acid—iodine System in N—C Bond Cleavage

A mixture of hypophosphorous acid(H3PO2)and iodine in acetic acid can cleave the N-alkyl bond in a variety of N-1 substituted pyrimidine derivative in relatively high yields,without any damage to the amido bond in the non-nucleosides pyrimidine base skeleton.     

FT-IR, FT-Raman spectra and quantum chemical calculations of some chloro substituted phenoxy acetic acids

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of o-chlorophenoxy acetic acid (OCPAA) and p-chlorophenoxy acetic acids (PCPAA). The FT-IR and Fourier transform-Raman spectra of both the compounds was recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods with 6-311++G(d,p) basis set and harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compounds were also performed at B3LYP/6-311++G(d,p) level of theory. A detailed interpretation of the infrared and Raman spectra of o-chloro and p-chlorophenoxy acetic acid is reported. The theoretical FT-IR spectrograms for the title molecules have been constructed.     

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–HgII–T Base Pairs

The metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–Hg^II–T base pairs. The Hg^II ion occupies the center between two T residues. The N3‐Hg^II bond distance is 2.0 Å. The relatively short Hg^II‐Hg^II distance (3.3 Å) observed in consecutive T–Hg^II–T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B‐form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg^II. The structure of the metallo DNA duplex itself and the Hg^II‐induced structural switching from the nonhelical form to the B‐form provide the basis for structure‐based design of metal‐conjugated nucleic acid nanomaterials.     

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.     

Conformational properties of thiophene oligomers

The molecular geometries and the torsional potentials about the inter‐ring C‐C bond in α‐oligothiophenes (α‐nTh, n=2–4) have been calculated by means of conventional ab initio and density functional theory (DFT) calculations employing the hybrid B3LYP and BH&HLYP functionals. The position and the energetics of the critical points in the potential energy curve generated by rotation about the inter‐ring C? C bond are shown to be dependent on the computational method. DFT calculations, in comparison with MP2 calculations, favour conjugative interactions, while steric and coulombic interactions are equally treated by both methods. On oligomerization the electron delocalisation increases slightly, the p‐charge being preferentially confined within the rings, although it is sufficient to move the molecular structure towards co‐planarization and to increase the barrier through the perpendicular conformation. The IR and Raman spectra on the relevant rotamers of α‐2Th have been computed at HF/6–31G* and B3LYP/6–31G* levels. The comparison with the experiment is excellent. It has been found that small twisting from the planar conformation has no apparent effects, while 90° twisting and isomerization to the syn‐gauche form produce significant frequency and intensity variations which could be useful probes in conformational studies. The simulated IR and Raman spectra of the α‐2Th rotamers are consistent with a smallπ‐electron delocalisation between the rings.     

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) Th     

Cd2+离子诱导的DNA构象变化

近年来,Cd^2 由于其在生物化学、临床医学、环境和农业科学等领域的重要性而受到了极大的关注^[1]。同其它金属离子一样,Cd^2 离子能与蛋白和其它生物分子反应从而影响动物和人类的器官,如肺、前列腺、睾丸、心脏、肝和肾等的正常生理活动^[2-4]。日本的痛痛病就是由于Cd^2 引起的骨软化和肾小管功能障碍造成的。但是从分子水平上对Cd^2 与生物大分子的相互作用机制的研究还较少。本文对Cd^2 与鲑鱼精DNA的相互作用及其对DNA构象的影响进行了初步研究。结果表明,Cd^2 可与DNA发生作用,并且使DNA构象发生变化。