DNA编码序列的图形表示及相似度计算

将DNA编码序列转化为图,然后计算得图的不变量-分子连接性指数,由所得的拓扑指数对DNA编码序列进行相似度比较以确认其同源性,得到了较好的结果.     

半合成人肿瘤坏死因子cDNA的构建及其在大肠杆菌中的高表达

本文报道从人基因文库中分离淋巴毒素(LT)基因的同时,克隆了肿瘤坏死因子(TNF)基因,这两个基因相距1.2kb.TNF基因有4个外显子,第4外显子编码TNF成熟蛋白157个氨基酸中的140个.将第4外显子切出一部分,再人工合成编码其余氨基酸的DNA片段,两者连接构成重组的人TNF(rhTNF)cDNA,并克隆在大肠杆菌表达载体中成功地得到表达.5 l罐发酵得菌体约20g/l,以L929为靶细胞测定细胞毒活性为10~6-10~7单位/ml.高压液相色谱仪分离纯化rhTNF,冻干后得白色粉剂.测定了这种rhTNF的氨基端的10个氨基酸序列,证明与天然的人TNF完全相同.纯度约为95％.     

一种具有规则结构的蛋白单体之间相互识别的分子力学模拟和量子化学计算

使用分子力学、分子动态学以及量子化学计算方法, 对天然的昆虫抗冻蛋白质分子(TmAFP)以长轴平行的方式发生二体相互作用的可能模式进行了系统研究. 分子模拟的结果表明, 在可能的相互作用模式中, 其相互作用区域必须至少包含一个β-面, 并且当蛋白单体均取β-面靠近时, 其侧链上的羟基在空间的分布满足结构上的二维匹配; 利用分子力学与量子化学相结合的方法得到的结果表明两单体的β-面之间具有相对最强的相互作用, 同时, 高级别的DFT计算以及van der Waals键电荷密度分析进一步证实β-面的相互识别主要表现为β-面的一个苏氨酸侧链的羟基对另一个的苏氨酸羟基氧的识别, 即它们之间能形成较强的氢键. 因此, 分子力学以及量子化学的计算结果都说明蛋白单体在相互识别的过程中, 均以β-面相互作用的可能性最大.     

α/β类蛋白折叠中π-π相互作用的特异性

以α/β类蛋白的2种典型折叠类型为研究对象,对205个低相似度蛋白样本中的π-π相互作用进行统计分析.计算结果表明,(α/β)8-barrel折叠中π-π相互作用的分布密度高于经典Rossmann折叠,且在关键的局部区域的差异更加显著;芳香族氨基酸在(α/β)8-barrel结构中更容易形成π-π相互作用;色氨酸对应的3种π-π相互作用组合在(α/β)8-barrel折叠中出现的几率显著高于经典Rossmann折叠;(α/β)8-barrel折叠中π-π相互作用形成复杂π网络的能力强于经典Rossmann折叠.上述结果表明,π-π相互作用在α/β类蛋白的不同折叠类型中存在特异性,其在稳定(α/β)8-barrel结构中的作用强于经典Rossmann折叠.     

PML基因的组织结构及在早幼粒白血病中的分子重组

本文报道了与急性早幼粒细胞白血病(APL)t(15;17)易位中有关的PML基因的结构。该基因长约50kb,由7个“主体外显子”(P_1—P_7)及几个可供不同剪接的3′端外显子及相应的内含子构成。其基因组织结构及蛋白质的功能区有明显的结构功能对应关系。于t(15;17)中,15号染色体的断裂点丛集于三个区域即PML-bcr1,PML-bcr2和PML-bcr3。PML-(bcr1+bcr2)与PML-bcr3之间的区域间隔为10kb,由此产生不同的外显子-内含子结构,导致PML基因的不同部分与位于17号染色体的部分RARα基因连接,后者的断裂点恒定地位于第二内含子中。PML基因断裂部位的差异是构成二种主要的PML-RARα融合mRNA异构体的分子基础:长(L)型异构体由PML1—6外显子与RARα编码B_F区域的外显子组成;短(S)型异构体由PML的三个外显子(P_1—P_3)与上述相同成分的RARα外显子剪接构成。顺序分析显示,在PML的7个“主体”外显子中,仅P_3和P_6与RARα外显子3的剪接能维持融合基因的阅读框架。     

温度及pH敏感的β-环糊精聚合物微球的合成及药物控制释放研究

以反相乳液聚合得到了β-CD聚合物微球,对β-CD微球进行氯乙酰化改性后,利用原子转移自由基聚合的方法把聚甲基丙烯酸N ,N 二甲氨基乙酯(PDMAEMA)接枝到β-CD微球上,从而得到了具有温度和pH响应性的β- CD聚合物微球.通过红外光谱、元素分析确定了PDMAEMA接枝的β- CD微球的结构,采用热台偏光显微镜直接观测到了β- CD微球的温度和pH敏感性.对模型药物染料木素(GNT)和苯丁酸氮芥(CLB )进行了控制释放研究,结果表明pH值可对微球的“内环境”起到“开 关”作用,从而可构筑出一种新型的药物控制释放体系.     

W/O乳化法制备明胶/β-磷酸三钙多孔复合微球及其热学性能

采用乳液、离子缔合法制备得到明胶(Gel)/β-纳米磷酸三钙(β-TCP)复合多孔微球,其尺寸可通过控制反应的搅拌速度进行调节. SEM和光学显微镜观察表明,明胶/β-TCP复合微球尺寸在20～40 μm之间,被包敷的磷酸三钙为200 nm左右,微球内部呈多孔结构. 当m(磷酸三钙)∶m(明胶)＞0.4∶1时,有大量花瓣状晶体附着于复合微球的表面,是磷酸三钙溶解和明胶分子诱导重结晶所致. XRD与IR图谱表明,磷酸三钙纳米粒子与明胶之间存在化学键合,明胶/β-纳米磷酸三钙复合微球的微观结构与自然骨相似. DSC-TGA结果显示,90%的TCP在乳化过程中与明胶复合. 本文所制备的复合微球,为添加各种药物和促骨生长因子并实现缓释提供了优良的载体.     

β-环糊精微球对染料分子吸附作用研究

以环氧氯丙烷为交联剂,采取反相乳液聚合得到β-环糊精微球(EPI-β-CD),经丁二酸酐酰化后得到微球表面具有羧基的β-环糊精微球(SUC-EPI-β-CD),分别采用红外光谱、扫描电镜和激光粒度分析仪表征了其结构及形貌特征.选择染料亚甲基蓝(MB)和甲基橙(MO)作为模型分子,考察了所合成微球的吸附性能.结果表明:由于β-CD与两种染料分子的相互作用力不同,微球EPI-β-CD吸附亚甲基兰染料的能力强于甲基橙;两种微球对MB的吸附等温数据与Freundlich方程拟合较好,且均为优惠吸附;羧丁基酰化β-环糊精微球(SUC-EPI-β-CD)表现出较明显的pH敏感性.     

铜催化对C-C不饱和键铜氢化引发的多米诺反应

总结了由铜催化的对C-C不饱和键铜氢化反应引发的多米诺反应,反应过程包括铜氢活性物种的产生、对C-C不饱和键的加成及铜氢物种的再生,其中的C-C不饱和键来源于α,β-不饱和酮、α,β-不饱和羧酸酯、芳基烯烃、脂族族烯烃以及炔烃.反应中氢硅烷作为氢负离子源,铜氢化反应产生的中间体随后对极性不饱和键如羰基和亚胺进行加成反应或对饱和键进行取代反应,最终生成两个或多个化学键.反应不需要对中间产物进行纯化,也不需要改变操作条件,方法简洁高效,在有机合成中有重要的应用价值.     

一种新的混合斑精子分离方法

制备了精子表面膜抗原受精素β蛋白(Fertilinβ)的特异性抗体,通过抗原-抗体反应和抗体固相偶联技术,将抗体连接到琼脂糖球珠上,建立了混合斑精子分离纯化的新方法.首先,通过聚合酶链式反应(PCR)扩增编码人受精素β蛋白第341~373位氨基酸的基因序列,构建PGEX-4T-1/Fertilinβ原核表达质粒;其次,诱导表达GST-Fertilinβ融合蛋白,制备受精素β蛋白多克隆抗体,免疫荧光检测结果表明,受精素β蛋白定位于精子的头后部,并且阴道上皮细胞没有受精素β蛋白的表达;最后,将受精素β抗体与ProteinA琼脂糖球珠连接构建固相抗体系统,将精子吸附于表面,可从混合斑(精子与阴道上皮细胞混合液)中分离纯化精子.本文为性犯罪案件侦破提供了新的方法.     

Linear regression model of DNA sequences and its application

We constructed six new models to analyze the DNA sequences. First, we regarded a DNA primary sequence as a random process in t and gave three ways to define nucleotides' random distribution functions. We extracted some parameters from the linear model and analyzed the changes of the nucleotides' distributions. In order to facilitate the comparison of DNA sequences, we proposed two ways to measure their similarities. Finally, we compared the six models by analyzing the similarities of the DNA primary sequences presented in Table 1 and selected the optimal one.     

Numerical characterization of DNA sequences based on the k-step Markov chain transition probability

A DNA sequence can be regarded as a discrete-time Markov chain. Based on k-step transition probabilities, we construct a series of 4 x 4 k-step transition matrices to characterize the DNA primary sequences. According to the properties of Markov chains, we obtain distributions of A, T, C and G, and analyze the changes among them from yesterday to tomorrow. We can calculate the probabilities of nucleotide triples of DNA primary sequences. Finally, we introduce a correlation of this kind of transition matrices and consider it as an invariant to analyze the similarities/dissimilarities of DNA sequences.     

Using Huffman coding method to visualize and analyze DNA sequences

On the basis of the Huffman coding method, we propose a new graphical representation of DNA sequence. The representation can avoid degeneracy and loss of information in the transfer of data from a DNA sequence to its graphical representation. Then a multicomponent vector from the representation is introduced to characterize quantitatively DNA sequences. The components of the vector are derived from the graphical representation of DNA primary sequence. The examination of similarities and dissimilarities among the complete coding sequences of β-globin gene of 11 species and six ND6 proteins shows the utility of the scheme.     

Condensed representation of DNA primary sequences

With rapid reporting of DNA sequences derived from automated DNA sequencing techniques, the problem of reviewing and ordering such information has become acute. We have introduced a condensed representation of primary sequences of DNA that offers an alternative method of registering DNA. The advantage of the condensed codes for DNA is that it not only offers fast, qualitative comparisons of DNA but also allows quantitative comparisons of DNA from different sources. The approach is outlined for a particular human beta globin sequence extract. Using the condensed representation of the primary DNA sequences, comparisons are made between primary sequences for Exon 1 of human beta globin and seven other beta globins.     

Syntheses, structures and reactivities of designed analogues of cobalt(III)- bleomycinsz : Insight into the mechanism of sequence-specific DNA cleavage upon illumination

Three Co (III) complexes of a designed ligand PMAH that mimics the metal-binding domain of the antitumor antibioticbleomycin (BLM) have been isolated and structurally characterized. The coordination structures of the various forms of Co(III)-BLMs have been established on the basis of spectral similarities between these synthetic analogues and the corresponding Co(III)-BLMs. All three analogues, like Co(III)-BLMs, induce DNA strand scission upon UV illumination. Both DNA cleavage and spin trapping experiments demonstrate that UV irradiation of the analogues generates a C/N-based radical on the ligand framework which rapidly reacts with water to produce -OH radical near the DNA helix and causes strand scission. A similar mechanism could account for the photoactivity of the Co(III)-BLMs. Covalent attachment of DNA-binding groups to these analogues enhances the DNA-affinities and photocleavage efficiencies to a great extent. The hybrid analogues promote sequence-specific DNA photodamage at micromolar concentrations. The metallated cores of the hybrid analogues are the primary determinant of the observed sequence-specificity. Details of the mode of binding of the hybrid analogues to DNA have been explored by NMR techniques.     

Synthesis, characterization, and remarkable biological properties of cyclodextrins bearing guanidinoalkylamino and aminoalkylamino groups on their primary side

The introduction of aminoalkylamino and guanidinoalkylamino substituents on the primary side of beta- and gamma-cyclodextrin (CDs) resulted in a series of novel compounds that were extensively characterized by NMR spectroscopy and mass spectrometry. Bromination of the primary side of beta- and gamma-CD, and reaction with neat alkylene diamines at a pressure of 7 atm afforded aminoalkylamino derivatives that were then guanylated at the primary amino group to give the corresponding guanidinoalkylamino-CDs. These compounds are water soluble and display pK(a) values that allow them to be mostly protonated at neutral pH; for example, pK(a(1)) approximately 6.4 and pK(a(2)) approximately 9.5 for the aminoethylamino-beta-CD and pK(a(1)) approximately 7.8 and pK(a(2)) approximately 11.0 for the guanidinoethylamino-beta-CD. The title CDs are rigid, cyclic alpha-D-glucopyranose oligomers (heptamers or octamers) with branches that resemble lysine and arginine side chains that enable multiple interactions with suitable substrates. Thus, they bear similarities to known cell-penetrating peptides. Indeed, the compounds were found to cross the membranes of HeLa cells and penetrate inside the cytoplasm quickly, the guadinylated ones within 15 min, as shown by fluorescence microscopy using fluorescein-labeled derivatives. The toxicity of the compounds, measured by performing MTT tests, ranged from 50 to 300 microM. Furthermore, some of the aminated CDs could facilitate the transfection of DNA expressing the green fluorescent protein (GFP) in HEK 293T cells, with effectiveness comparable to the commercial agent Lipofectamine 2000. Circular dichroism, atomic force microscopy and electrophoresis experiments confirmed the strong interaction of the compounds with DNA. Because of their carbohydrate, non-peptide nature the title compounds are not anticipated to be enzymatically labile or immunogenic, and thus they fulfill many of the criteria for non-hazardous transport vectors in biological and pharmaceutical applications.     

Kinetic mechanisms in morpholino-DNA surface hybridization

Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or "probe", species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e., duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

Fragmentation of fiberlike structures: sonication studies of cylindrical block copolymer micelles and behavioral comparisons to biological fibrils

In alkane solvents, poly(isoprene-b-ferrocenyldimethylsilane) (PI-b-PFS) block copolymer forms fiberlike micelles, which show intriguing similarities with biological fibers such as amyloid fibers. Both systems exhibit fiber growth by a nucleated self-assembly mechanism and rapidly fragment upon exposure to the shear forces of ultrasonic irradiation. Sonication of PI-b-PFS cylindrical micelles was studied quantitatively by static light scattering and by electron microscopy. Both techniques are in excellent agreement and show that the weight-average length of sonicated micelles decreases as a function of sonication time. Simulation of the cleavage of micelles using different scission models shows that micelle fragmentation follows a Gaussian model and that the scission is highly dependent on micelle length, in contrast to DNA and polymer chain scission. We speculate that biological fibers, which are similar in length and rigidity to PFS block copolymer micelles, fragment by a similar mechanism when subjected to sonication.